var_ngmlr_two_assemblies_tables.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Summarize the SV detected with two difference genome builds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "Attaching package: ‘dplyr’\n",
      "\n",
      "The following objects are masked from ‘package:data.table’:\n",
      "\n",
      "    between, first, last\n",
      "\n",
      "The following objects are masked from ‘package:stats’:\n",
      "\n",
      "    filter, lag\n",
      "\n",
      "The following objects are masked from ‘package:base’:\n",
      "\n",
      "    intersect, setdiff, setequal, union\n",
      "\n"
     ]
    }
   ],
   "source": [
    ".libPaths('/cluster/home/fangzi/R')\n",
    "library('ggplot2')\n",
    "library('data.table')\n",
    "library('dplyr')\n",
    "library('patchwork')\n",
    "setwd('/nfs/nas12.ethz.ch/fs1201/green_groups_tg_public/data/fang/Nanopore/sv_two_assembly/sv_ngmlr')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "12572"
      ],
      "text/latex": [
       "12572"
      ],
      "text/markdown": [
       "12572"
      ],
      "text/plain": [
       "[1] 12572"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "13295"
      ],
      "text/latex": [
       "13295"
      ],
      "text/markdown": [
       "13295"
      ],
      "text/plain": [
       "[1] 13295"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "12545"
      ],
      "text/latex": [
       "12545"
      ],
      "text/markdown": [
       "12545"
      ],
      "text/plain": [
       "[1] 12545"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "13052"
      ],
      "text/latex": [
       "13052"
      ],
      "text/markdown": [
       "13052"
      ],
      "text/plain": [
       "[1] 13052"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#read the data \n",
    "Angus=fread('angus_variants_ngmlr.csv')\n",
    "UCD=fread('UCD_variants_ngmlr.csv')\n",
    "nrow(Angus)\n",
    "nrow(UCD)\n",
    "\n",
    "#check number of the variants in autosomes (chr1:29)\n",
    "nrow(Angus[CHROM!='Y'])\n",
    "nrow(UCD[CHROM!='X'])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 6 × 9</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ID</th><th scope=col>REF</th><th scope=col>ALT</th><th scope=col>QUAL</th><th scope=col>SVLEN</th><th scope=col>SVTYPE</th><th scope=col>CSQ</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>1</td><td> 33683</td><td>0</td><td>CCCAGAGGAGAAAGCATCACTAAAAGCCTGGAGACTCTGGTAAAGGCACCACTTT</td><td>N                                                                                                                                                           </td><td> 8</td><td>-54</td><td>DEL</td><td>deletion|downstream_gene_variant|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding|||||||||||1767|-1||HGNC|KAT2B|||                </td></tr>\n",
       "\t<tr><td>1</td><td> 90953</td><td>2</td><td><span style=white-space:pre-wrap>N                                                      </span></td><td>CCGCGAGGGTCTCTTGGGGGCCATGTAGGGTCTCTGGGAGGCTGACAGGGTGTCCCCAAGGCCGCGAGGGTCTCTGGAGGTCGCCAGGGCCTCCCGGGGCCGCGAGGGTCTCTGGGGGGCCATGAGGGTCTCTGGGTAAATAAGTGAGGGTCTCTG</td><td>14</td><td>124</td><td>INS</td><td>insertion|intron_variant&amp;feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||6|0.01</td></tr>\n",
       "\t<tr><td>1</td><td> 92223</td><td>3</td><td><span style=white-space:pre-wrap>N                                                      </span></td><td><span style=white-space:pre-wrap>TTCTCCCAGGGAGGTACTGTGAGCCTGCCCACCTGTGAATGACCCTGCCCCACTGCCTCTCTTAAACTAAAGAGCCCAGTTTCGC                                                                       </span></td><td>16</td><td> 81</td><td>INS</td><td>insertion|intron_variant&amp;feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||5|0.01</td></tr>\n",
       "\t<tr><td>1</td><td>132889</td><td>4</td><td><span style=white-space:pre-wrap>CGGGGCGCGCAGGTCCCCGAGCGGGGCTCCCAGGGACCCGCTCCGCTCCCG    </span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                           </span></td><td>22</td><td>-51</td><td>DEL</td><td>deletion|intron_variant&amp;feature_truncation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||1/17||||||||||-1||HGNC|KAT2B||51|0.05</td></tr>\n",
       "\t<tr><td>1</td><td>265265</td><td>5</td><td><span style=white-space:pre-wrap>N                                                      </span></td><td><span style=white-space:pre-wrap>GCGGGGCATCACGGAGCTGGTGGCGGCAGCGGGGCATCACGGGAGCTGGTGGGGCAGGGTGCATCACGGGAGCTGGTCGAGGGCAGGCATCATGGAGCTGGTGGGGCAGGGGTGCATCACGGAGCTGGTCGTGGGCAGGGTGCA            </span></td><td> 7</td><td>150</td><td>INS</td><td><span style=white-space:pre-wrap>insertion|intron_variant&amp;feature_elongation|MODIFIER|EFHB|ENSBIXG00000028467|Transcript|ENSBIXT00000043467|protein_coding||8/12||||||||||1||HGNC|EFHB||4|0.01   </span></td></tr>\n",
       "\t<tr><td>1</td><td>294608</td><td>7</td><td>N                                                      </td><td>CGTGGCACAGGCTCTCTCTCCAGTTGCAGGGAGCAGGGCTCATCTCCGGGTGGTGGTTCCCTTGAGTGTGG                                                                                     </td><td> 7</td><td> 71</td><td>INS</td><td>insertion|intergenic_variant|MODIFIER|||||||||||||||||||||||                                                                                                    </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 6 × 9\n",
       "\\begin{tabular}{r|lllllllll}\n",
       " CHROM & POS & ID & REF & ALT & QUAL & SVLEN & SVTYPE & CSQ\\\\\n",
       " <chr> & <int> & <chr> & <chr> & <chr> & <dbl> & <int> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t 1 &  33683 & 0 & CCCAGAGGAGAAAGCATCACTAAAAGCCTGGAGACTCTGGTAAAGGCACCACTTT & N                                                                                                                                                            &  8 & -54 & DEL & deletion\\textbar{}downstream\\_gene\\_variant\\textbar{}MODIFIER\\textbar{}KAT2B\\textbar{}ENSBIXG00000005942\\textbar{}Transcript\\textbar{}ENSBIXT00000043470\\textbar{}protein\\_coding\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}1767\\textbar{}-1\\textbar{}\\textbar{}HGNC\\textbar{}KAT2B\\textbar{}\\textbar{}\\textbar{}                \\\\\n",
       "\t 1 &  90953 & 2 & N                                                       & CCGCGAGGGTCTCTTGGGGGCCATGTAGGGTCTCTGGGAGGCTGACAGGGTGTCCCCAAGGCCGCGAGGGTCTCTGGAGGTCGCCAGGGCCTCCCGGGGCCGCGAGGGTCTCTGGGGGGCCATGAGGGTCTCTGGGTAAATAAGTGAGGGTCTCTG & 14 & 124 & INS & insertion\\textbar{}intron\\_variant\\&feature\\_elongation\\textbar{}MODIFIER\\textbar{}KAT2B\\textbar{}ENSBIXG00000005942\\textbar{}Transcript\\textbar{}ENSBIXT00000043470\\textbar{}protein\\_coding\\textbar{}\\textbar{}2/17\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}-1\\textbar{}\\textbar{}HGNC\\textbar{}KAT2B\\textbar{}\\textbar{}6\\textbar{}0.01\\\\\n",
       "\t 1 &  92223 & 3 & N                                                       & TTCTCCCAGGGAGGTACTGTGAGCCTGCCCACCTGTGAATGACCCTGCCCCACTGCCTCTCTTAAACTAAAGAGCCCAGTTTCGC                                                                        & 16 &  81 & INS & insertion\\textbar{}intron\\_variant\\&feature\\_elongation\\textbar{}MODIFIER\\textbar{}KAT2B\\textbar{}ENSBIXG00000005942\\textbar{}Transcript\\textbar{}ENSBIXT00000043470\\textbar{}protein\\_coding\\textbar{}\\textbar{}2/17\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}-1\\textbar{}\\textbar{}HGNC\\textbar{}KAT2B\\textbar{}\\textbar{}5\\textbar{}0.01\\\\\n",
       "\t 1 & 132889 & 4 & CGGGGCGCGCAGGTCCCCGAGCGGGGCTCCCAGGGACCCGCTCCGCTCCCG     & N                                                                                                                                                            & 22 & -51 & DEL & deletion\\textbar{}intron\\_variant\\&feature\\_truncation\\textbar{}MODIFIER\\textbar{}KAT2B\\textbar{}ENSBIXG00000005942\\textbar{}Transcript\\textbar{}ENSBIXT00000043470\\textbar{}protein\\_coding\\textbar{}\\textbar{}1/17\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}-1\\textbar{}\\textbar{}HGNC\\textbar{}KAT2B\\textbar{}\\textbar{}51\\textbar{}0.05\\\\\n",
       "\t 1 & 265265 & 5 & N                                                       & GCGGGGCATCACGGAGCTGGTGGCGGCAGCGGGGCATCACGGGAGCTGGTGGGGCAGGGTGCATCACGGGAGCTGGTCGAGGGCAGGCATCATGGAGCTGGTGGGGCAGGGGTGCATCACGGAGCTGGTCGTGGGCAGGGTGCA             &  7 & 150 & INS & insertion\\textbar{}intron\\_variant\\&feature\\_elongation\\textbar{}MODIFIER\\textbar{}EFHB\\textbar{}ENSBIXG00000028467\\textbar{}Transcript\\textbar{}ENSBIXT00000043467\\textbar{}protein\\_coding\\textbar{}\\textbar{}8/12\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}1\\textbar{}\\textbar{}HGNC\\textbar{}EFHB\\textbar{}\\textbar{}4\\textbar{}0.01   \\\\\n",
       "\t 1 & 294608 & 7 & N                                                       & CGTGGCACAGGCTCTCTCTCCAGTTGCAGGGAGCAGGGCTCATCTCCGGGTGGTGGTTCCCTTGAGTGTGG                                                                                      &  7 &  71 & INS & insertion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                                                    \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 6 × 9\n",
       "\n",
       "| CHROM &lt;chr&gt; | POS &lt;int&gt; | ID &lt;chr&gt; | REF &lt;chr&gt; | ALT &lt;chr&gt; | QUAL &lt;dbl&gt; | SVLEN &lt;int&gt; | SVTYPE &lt;chr&gt; | CSQ &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|\n",
       "| 1 |  33683 | 0 | CCCAGAGGAGAAAGCATCACTAAAAGCCTGGAGACTCTGGTAAAGGCACCACTTT | N                                                                                                                                                            |  8 | -54 | DEL | deletion|downstream_gene_variant|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding|||||||||||1767|-1||HGNC|KAT2B|||                 |\n",
       "| 1 |  90953 | 2 | N                                                       | CCGCGAGGGTCTCTTGGGGGCCATGTAGGGTCTCTGGGAGGCTGACAGGGTGTCCCCAAGGCCGCGAGGGTCTCTGGAGGTCGCCAGGGCCTCCCGGGGCCGCGAGGGTCTCTGGGGGGCCATGAGGGTCTCTGGGTAAATAAGTGAGGGTCTCTG | 14 | 124 | INS | insertion|intron_variant&amp;feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||6|0.01 |\n",
       "| 1 |  92223 | 3 | N                                                       | TTCTCCCAGGGAGGTACTGTGAGCCTGCCCACCTGTGAATGACCCTGCCCCACTGCCTCTCTTAAACTAAAGAGCCCAGTTTCGC                                                                        | 16 |  81 | INS | insertion|intron_variant&amp;feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||5|0.01 |\n",
       "| 1 | 132889 | 4 | CGGGGCGCGCAGGTCCCCGAGCGGGGCTCCCAGGGACCCGCTCCGCTCCCG     | N                                                                                                                                                            | 22 | -51 | DEL | deletion|intron_variant&amp;feature_truncation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||1/17||||||||||-1||HGNC|KAT2B||51|0.05 |\n",
       "| 1 | 265265 | 5 | N                                                       | GCGGGGCATCACGGAGCTGGTGGCGGCAGCGGGGCATCACGGGAGCTGGTGGGGCAGGGTGCATCACGGGAGCTGGTCGAGGGCAGGCATCATGGAGCTGGTGGGGCAGGGGTGCATCACGGAGCTGGTCGTGGGCAGGGTGCA             |  7 | 150 | INS | insertion|intron_variant&amp;feature_elongation|MODIFIER|EFHB|ENSBIXG00000028467|Transcript|ENSBIXT00000043467|protein_coding||8/12||||||||||1||HGNC|EFHB||4|0.01    |\n",
       "| 1 | 294608 | 7 | N                                                       | CGTGGCACAGGCTCTCTCTCCAGTTGCAGGGAGCAGGGCTCATCTCCGGGTGGTGGTTCCCTTGAGTGTGG                                                                                      |  7 |  71 | INS | insertion|intergenic_variant|MODIFIER|||||||||||||||||||||||                                                                                                     |\n",
       "\n"
      ],
      "text/plain": [
       "  CHROM POS    ID REF                                                    \n",
       "1 1      33683 0  CCCAGAGGAGAAAGCATCACTAAAAGCCTGGAGACTCTGGTAAAGGCACCACTTT\n",
       "2 1      90953 2  N                                                      \n",
       "3 1      92223 3  N                                                      \n",
       "4 1     132889 4  CGGGGCGCGCAGGTCCCCGAGCGGGGCTCCCAGGGACCCGCTCCGCTCCCG    \n",
       "5 1     265265 5  N                                                      \n",
       "6 1     294608 7  N                                                      \n",
       "  ALT                                                                                                                                                         \n",
       "1 N                                                                                                                                                           \n",
       "2 CCGCGAGGGTCTCTTGGGGGCCATGTAGGGTCTCTGGGAGGCTGACAGGGTGTCCCCAAGGCCGCGAGGGTCTCTGGAGGTCGCCAGGGCCTCCCGGGGCCGCGAGGGTCTCTGGGGGGCCATGAGGGTCTCTGGGTAAATAAGTGAGGGTCTCTG\n",
       "3 TTCTCCCAGGGAGGTACTGTGAGCCTGCCCACCTGTGAATGACCCTGCCCCACTGCCTCTCTTAAACTAAAGAGCCCAGTTTCGC                                                                       \n",
       "4 N                                                                                                                                                           \n",
       "5 GCGGGGCATCACGGAGCTGGTGGCGGCAGCGGGGCATCACGGGAGCTGGTGGGGCAGGGTGCATCACGGGAGCTGGTCGAGGGCAGGCATCATGGAGCTGGTGGGGCAGGGGTGCATCACGGAGCTGGTCGTGGGCAGGGTGCA            \n",
       "6 CGTGGCACAGGCTCTCTCTCCAGTTGCAGGGAGCAGGGCTCATCTCCGGGTGGTGGTTCCCTTGAGTGTGG                                                                                     \n",
       "  QUAL SVLEN SVTYPE\n",
       "1  8   -54   DEL   \n",
       "2 14   124   INS   \n",
       "3 16    81   INS   \n",
       "4 22   -51   DEL   \n",
       "5  7   150   INS   \n",
       "6  7    71   INS   \n",
       "  CSQ                                                                                                                                                             \n",
       "1 deletion|downstream_gene_variant|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding|||||||||||1767|-1||HGNC|KAT2B|||                \n",
       "2 insertion|intron_variant&feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||6|0.01\n",
       "3 insertion|intron_variant&feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||5|0.01\n",
       "4 deletion|intron_variant&feature_truncation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||1/17||||||||||-1||HGNC|KAT2B||51|0.05\n",
       "5 insertion|intron_variant&feature_elongation|MODIFIER|EFHB|ENSBIXG00000028467|Transcript|ENSBIXT00000043467|protein_coding||8/12||||||||||1||HGNC|EFHB||4|0.01   \n",
       "6 insertion|intergenic_variant|MODIFIER|||||||||||||||||||||||                                                                                                    "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 6 × 35</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ID</th><th scope=col>REF</th><th scope=col>ALT</th><th scope=col>QUAL</th><th scope=col>SVLEN</th><th scope=col>SVTYPE</th><th scope=col>CSQ</th><th scope=col>Allele</th><th scope=col>⋯</th><th scope=col>Codons</th><th scope=col>Existing_variation</th><th scope=col>DISTANCE</th><th scope=col>STRAND</th><th scope=col>FLAGS</th><th scope=col>SYMBOL_SOURCE</th><th scope=col>HGNC_ID</th><th scope=col>HGVS_OFFSET</th><th scope=col>OverlapBP</th><th scope=col>OverlapPC</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>⋯</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>1</td><td> 33683</td><td>0</td><td>CCCAGAGGAGAAAGCATCACTAAAAGCCTGGAGACTCTGGTAAAGGCACCACTTT</td><td>N                                                                                                                                                           </td><td> 8</td><td>-54</td><td>DEL</td><td>deletion|downstream_gene_variant|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding|||||||||||1767|-1||HGNC|KAT2B|||                </td><td>deletion </td><td>⋯</td><td></td><td></td><td>1767</td><td>-1</td><td></td><td>HGNC</td><td>KAT2B</td><td></td><td>  </td><td>NA  </td></tr>\n",
       "\t<tr><td>1</td><td> 90953</td><td>2</td><td><span style=white-space:pre-wrap>N                                                      </span></td><td>CCGCGAGGGTCTCTTGGGGGCCATGTAGGGTCTCTGGGAGGCTGACAGGGTGTCCCCAAGGCCGCGAGGGTCTCTGGAGGTCGCCAGGGCCTCCCGGGGCCGCGAGGGTCTCTGGGGGGCCATGAGGGTCTCTGGGTAAATAAGTGAGGGTCTCTG</td><td>14</td><td>124</td><td>INS</td><td>insertion|intron_variant&amp;feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||6|0.01</td><td>insertion</td><td>⋯</td><td></td><td></td><td><span style=white-space:pre-wrap>    </span></td><td>-1</td><td></td><td>HGNC</td><td>KAT2B</td><td></td><td>6 </td><td>0.01</td></tr>\n",
       "\t<tr><td>1</td><td> 92223</td><td>3</td><td><span style=white-space:pre-wrap>N                                                      </span></td><td><span style=white-space:pre-wrap>TTCTCCCAGGGAGGTACTGTGAGCCTGCCCACCTGTGAATGACCCTGCCCCACTGCCTCTCTTAAACTAAAGAGCCCAGTTTCGC                                                                       </span></td><td>16</td><td> 81</td><td>INS</td><td>insertion|intron_variant&amp;feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||5|0.01</td><td>insertion</td><td>⋯</td><td></td><td></td><td><span style=white-space:pre-wrap>    </span></td><td>-1</td><td></td><td>HGNC</td><td>KAT2B</td><td></td><td>5 </td><td>0.01</td></tr>\n",
       "\t<tr><td>1</td><td>132889</td><td>4</td><td><span style=white-space:pre-wrap>CGGGGCGCGCAGGTCCCCGAGCGGGGCTCCCAGGGACCCGCTCCGCTCCCG    </span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                           </span></td><td>22</td><td>-51</td><td>DEL</td><td>deletion|intron_variant&amp;feature_truncation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||1/17||||||||||-1||HGNC|KAT2B||51|0.05</td><td>deletion </td><td>⋯</td><td></td><td></td><td><span style=white-space:pre-wrap>    </span></td><td>-1</td><td></td><td>HGNC</td><td>KAT2B</td><td></td><td>51</td><td>0.05</td></tr>\n",
       "\t<tr><td>1</td><td>265265</td><td>5</td><td><span style=white-space:pre-wrap>N                                                      </span></td><td><span style=white-space:pre-wrap>GCGGGGCATCACGGAGCTGGTGGCGGCAGCGGGGCATCACGGGAGCTGGTGGGGCAGGGTGCATCACGGGAGCTGGTCGAGGGCAGGCATCATGGAGCTGGTGGGGCAGGGGTGCATCACGGAGCTGGTCGTGGGCAGGGTGCA            </span></td><td> 7</td><td>150</td><td>INS</td><td><span style=white-space:pre-wrap>insertion|intron_variant&amp;feature_elongation|MODIFIER|EFHB|ENSBIXG00000028467|Transcript|ENSBIXT00000043467|protein_coding||8/12||||||||||1||HGNC|EFHB||4|0.01   </span></td><td>insertion</td><td>⋯</td><td></td><td></td><td><span style=white-space:pre-wrap>    </span></td><td>1 </td><td></td><td>HGNC</td><td>EFHB </td><td></td><td>4 </td><td>0.01</td></tr>\n",
       "\t<tr><td>1</td><td>294608</td><td>7</td><td>N                                                      </td><td>CGTGGCACAGGCTCTCTCTCCAGTTGCAGGGAGCAGGGCTCATCTCCGGGTGGTGGTTCCCTTGAGTGTGG                                                                                     </td><td> 7</td><td> 71</td><td>INS</td><td>insertion|intergenic_variant|MODIFIER|||||||||||||||||||||||                                                                                                    </td><td>insertion</td><td>⋯</td><td></td><td></td><td>    </td><td>  </td><td></td><td>    </td><td>     </td><td></td><td>  </td><td>NA  </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 6 × 35\n",
       "\\begin{tabular}{r|lllllllllllllllllllllllllllllllllll}\n",
       " CHROM & POS & ID & REF & ALT & QUAL & SVLEN & SVTYPE & CSQ & Allele & Consequence & IMPACT & SYMBOL & Gene & Feature\\_type & Feature & BIOTYPE & EXON & INTRON & HGVSc & HGVSp & cDNA\\_position & CDS\\_position & Protein\\_position & Amino\\_acids & Codons & Existing\\_variation & DISTANCE & STRAND & FLAGS & SYMBOL\\_SOURCE & HGNC\\_ID & HGVS\\_OFFSET & OverlapBP & OverlapPC\\\\\n",
       " <chr> & <int> & <chr> & <chr> & <chr> & <dbl> & <int> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t 1 &  33683 & 0 & CCCAGAGGAGAAAGCATCACTAAAAGCCTGGAGACTCTGGTAAAGGCACCACTTT & N                                                                                                                                                            &  8 & -54 & DEL & deletion\\textbar{}downstream\\_gene\\_variant\\textbar{}MODIFIER\\textbar{}KAT2B\\textbar{}ENSBIXG00000005942\\textbar{}Transcript\\textbar{}ENSBIXT00000043470\\textbar{}protein\\_coding\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}1767\\textbar{}-1\\textbar{}\\textbar{}HGNC\\textbar{}KAT2B\\textbar{}\\textbar{}\\textbar{}                 & deletion  & downstream\\_gene\\_variant           & MODIFIER & KAT2B & ENSBIXG00000005942 & Transcript & ENSBIXT00000043470 & protein\\_coding &  &      &  &  &  &  &  &  &  &  & 1767 & -1 &  & HGNC & KAT2B &  &    & NA  \\\\\n",
       "\t 1 &  90953 & 2 & N                                                       & CCGCGAGGGTCTCTTGGGGGCCATGTAGGGTCTCTGGGAGGCTGACAGGGTGTCCCCAAGGCCGCGAGGGTCTCTGGAGGTCGCCAGGGCCTCCCGGGGCCGCGAGGGTCTCTGGGGGGCCATGAGGGTCTCTGGGTAAATAAGTGAGGGTCTCTG & 14 & 124 & INS & insertion\\textbar{}intron\\_variant\\&feature\\_elongation\\textbar{}MODIFIER\\textbar{}KAT2B\\textbar{}ENSBIXG00000005942\\textbar{}Transcript\\textbar{}ENSBIXT00000043470\\textbar{}protein\\_coding\\textbar{}\\textbar{}2/17\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}-1\\textbar{}\\textbar{}HGNC\\textbar{}KAT2B\\textbar{}\\textbar{}6\\textbar{}0.01 & insertion & intron\\_variant\\&feature\\_elongation & MODIFIER & KAT2B & ENSBIXG00000005942 & Transcript & ENSBIXT00000043470 & protein\\_coding &  & 2/17 &  &  &  &  &  &  &  &  &      & -1 &  & HGNC & KAT2B &  & 6  & 0.01\\\\\n",
       "\t 1 &  92223 & 3 & N                                                       & TTCTCCCAGGGAGGTACTGTGAGCCTGCCCACCTGTGAATGACCCTGCCCCACTGCCTCTCTTAAACTAAAGAGCCCAGTTTCGC                                                                        & 16 &  81 & INS & insertion\\textbar{}intron\\_variant\\&feature\\_elongation\\textbar{}MODIFIER\\textbar{}KAT2B\\textbar{}ENSBIXG00000005942\\textbar{}Transcript\\textbar{}ENSBIXT00000043470\\textbar{}protein\\_coding\\textbar{}\\textbar{}2/17\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}-1\\textbar{}\\textbar{}HGNC\\textbar{}KAT2B\\textbar{}\\textbar{}5\\textbar{}0.01 & insertion & intron\\_variant\\&feature\\_elongation & MODIFIER & KAT2B & ENSBIXG00000005942 & Transcript & ENSBIXT00000043470 & protein\\_coding &  & 2/17 &  &  &  &  &  &  &  &  &      & -1 &  & HGNC & KAT2B &  & 5  & 0.01\\\\\n",
       "\t 1 & 132889 & 4 & CGGGGCGCGCAGGTCCCCGAGCGGGGCTCCCAGGGACCCGCTCCGCTCCCG     & N                                                                                                                                                            & 22 & -51 & DEL & deletion\\textbar{}intron\\_variant\\&feature\\_truncation\\textbar{}MODIFIER\\textbar{}KAT2B\\textbar{}ENSBIXG00000005942\\textbar{}Transcript\\textbar{}ENSBIXT00000043470\\textbar{}protein\\_coding\\textbar{}\\textbar{}1/17\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}-1\\textbar{}\\textbar{}HGNC\\textbar{}KAT2B\\textbar{}\\textbar{}51\\textbar{}0.05 & deletion  & intron\\_variant\\&feature\\_truncation & MODIFIER & KAT2B & ENSBIXG00000005942 & Transcript & ENSBIXT00000043470 & protein\\_coding &  & 1/17 &  &  &  &  &  &  &  &  &      & -1 &  & HGNC & KAT2B &  & 51 & 0.05\\\\\n",
       "\t 1 & 265265 & 5 & N                                                       & GCGGGGCATCACGGAGCTGGTGGCGGCAGCGGGGCATCACGGGAGCTGGTGGGGCAGGGTGCATCACGGGAGCTGGTCGAGGGCAGGCATCATGGAGCTGGTGGGGCAGGGGTGCATCACGGAGCTGGTCGTGGGCAGGGTGCA             &  7 & 150 & INS & insertion\\textbar{}intron\\_variant\\&feature\\_elongation\\textbar{}MODIFIER\\textbar{}EFHB\\textbar{}ENSBIXG00000028467\\textbar{}Transcript\\textbar{}ENSBIXT00000043467\\textbar{}protein\\_coding\\textbar{}\\textbar{}8/12\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}1\\textbar{}\\textbar{}HGNC\\textbar{}EFHB\\textbar{}\\textbar{}4\\textbar{}0.01    & insertion & intron\\_variant\\&feature\\_elongation & MODIFIER & EFHB  & ENSBIXG00000028467 & Transcript & ENSBIXT00000043467 & protein\\_coding &  & 8/12 &  &  &  &  &  &  &  &  &      & 1  &  & HGNC & EFHB  &  & 4  & 0.01\\\\\n",
       "\t 1 & 294608 & 7 & N                                                       & CGTGGCACAGGCTCTCTCTCCAGTTGCAGGGAGCAGGGCTCATCTCCGGGTGGTGGTTCCCTTGAGTGTGG                                                                                      &  7 &  71 & INS & insertion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                                                     & insertion & intergenic\\_variant                & MODIFIER &       &                    &            &                    &                &  &      &  &  &  &  &  &  &  &  &      &    &  &      &       &  &    & NA  \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 6 × 35\n",
       "\n",
       "| CHROM &lt;chr&gt; | POS &lt;int&gt; | ID &lt;chr&gt; | REF &lt;chr&gt; | ALT &lt;chr&gt; | QUAL &lt;dbl&gt; | SVLEN &lt;int&gt; | SVTYPE &lt;chr&gt; | CSQ &lt;chr&gt; | Allele &lt;chr&gt; | ⋯ ⋯ | Codons &lt;chr&gt; | Existing_variation &lt;chr&gt; | DISTANCE &lt;chr&gt; | STRAND &lt;chr&gt; | FLAGS &lt;chr&gt; | SYMBOL_SOURCE &lt;chr&gt; | HGNC_ID &lt;chr&gt; | HGVS_OFFSET &lt;chr&gt; | OverlapBP &lt;chr&gt; | OverlapPC &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| 1 |  33683 | 0 | CCCAGAGGAGAAAGCATCACTAAAAGCCTGGAGACTCTGGTAAAGGCACCACTTT | N                                                                                                                                                            |  8 | -54 | DEL | deletion|downstream_gene_variant|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding|||||||||||1767|-1||HGNC|KAT2B|||                 | deletion  | ⋯ | <!----> | <!----> | 1767 | -1 | <!----> | HGNC | KAT2B | <!----> | <!----> | NA   |\n",
       "| 1 |  90953 | 2 | N                                                       | CCGCGAGGGTCTCTTGGGGGCCATGTAGGGTCTCTGGGAGGCTGACAGGGTGTCCCCAAGGCCGCGAGGGTCTCTGGAGGTCGCCAGGGCCTCCCGGGGCCGCGAGGGTCTCTGGGGGGCCATGAGGGTCTCTGGGTAAATAAGTGAGGGTCTCTG | 14 | 124 | INS | insertion|intron_variant&amp;feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||6|0.01 | insertion | ⋯ | <!----> | <!----> | <!----> | -1 | <!----> | HGNC | KAT2B | <!----> | 6  | 0.01 |\n",
       "| 1 |  92223 | 3 | N                                                       | TTCTCCCAGGGAGGTACTGTGAGCCTGCCCACCTGTGAATGACCCTGCCCCACTGCCTCTCTTAAACTAAAGAGCCCAGTTTCGC                                                                        | 16 |  81 | INS | insertion|intron_variant&amp;feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||5|0.01 | insertion | ⋯ | <!----> | <!----> | <!----> | -1 | <!----> | HGNC | KAT2B | <!----> | 5  | 0.01 |\n",
       "| 1 | 132889 | 4 | CGGGGCGCGCAGGTCCCCGAGCGGGGCTCCCAGGGACCCGCTCCGCTCCCG     | N                                                                                                                                                            | 22 | -51 | DEL | deletion|intron_variant&amp;feature_truncation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||1/17||||||||||-1||HGNC|KAT2B||51|0.05 | deletion  | ⋯ | <!----> | <!----> | <!----> | -1 | <!----> | HGNC | KAT2B | <!----> | 51 | 0.05 |\n",
       "| 1 | 265265 | 5 | N                                                       | GCGGGGCATCACGGAGCTGGTGGCGGCAGCGGGGCATCACGGGAGCTGGTGGGGCAGGGTGCATCACGGGAGCTGGTCGAGGGCAGGCATCATGGAGCTGGTGGGGCAGGGGTGCATCACGGAGCTGGTCGTGGGCAGGGTGCA             |  7 | 150 | INS | insertion|intron_variant&amp;feature_elongation|MODIFIER|EFHB|ENSBIXG00000028467|Transcript|ENSBIXT00000043467|protein_coding||8/12||||||||||1||HGNC|EFHB||4|0.01    | insertion | ⋯ | <!----> | <!----> | <!----> | 1  | <!----> | HGNC | EFHB  | <!----> | 4  | 0.01 |\n",
       "| 1 | 294608 | 7 | N                                                       | CGTGGCACAGGCTCTCTCTCCAGTTGCAGGGAGCAGGGCTCATCTCCGGGTGGTGGTTCCCTTGAGTGTGG                                                                                      |  7 |  71 | INS | insertion|intergenic_variant|MODIFIER|||||||||||||||||||||||                                                                                                     | insertion | ⋯ | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | NA   |\n",
       "\n"
      ],
      "text/plain": [
       "  CHROM POS    ID REF                                                    \n",
       "1 1      33683 0  CCCAGAGGAGAAAGCATCACTAAAAGCCTGGAGACTCTGGTAAAGGCACCACTTT\n",
       "2 1      90953 2  N                                                      \n",
       "3 1      92223 3  N                                                      \n",
       "4 1     132889 4  CGGGGCGCGCAGGTCCCCGAGCGGGGCTCCCAGGGACCCGCTCCGCTCCCG    \n",
       "5 1     265265 5  N                                                      \n",
       "6 1     294608 7  N                                                      \n",
       "  ALT                                                                                                                                                         \n",
       "1 N                                                                                                                                                           \n",
       "2 CCGCGAGGGTCTCTTGGGGGCCATGTAGGGTCTCTGGGAGGCTGACAGGGTGTCCCCAAGGCCGCGAGGGTCTCTGGAGGTCGCCAGGGCCTCCCGGGGCCGCGAGGGTCTCTGGGGGGCCATGAGGGTCTCTGGGTAAATAAGTGAGGGTCTCTG\n",
       "3 TTCTCCCAGGGAGGTACTGTGAGCCTGCCCACCTGTGAATGACCCTGCCCCACTGCCTCTCTTAAACTAAAGAGCCCAGTTTCGC                                                                       \n",
       "4 N                                                                                                                                                           \n",
       "5 GCGGGGCATCACGGAGCTGGTGGCGGCAGCGGGGCATCACGGGAGCTGGTGGGGCAGGGTGCATCACGGGAGCTGGTCGAGGGCAGGCATCATGGAGCTGGTGGGGCAGGGGTGCATCACGGAGCTGGTCGTGGGCAGGGTGCA            \n",
       "6 CGTGGCACAGGCTCTCTCTCCAGTTGCAGGGAGCAGGGCTCATCTCCGGGTGGTGGTTCCCTTGAGTGTGG                                                                                     \n",
       "  QUAL SVLEN SVTYPE\n",
       "1  8   -54   DEL   \n",
       "2 14   124   INS   \n",
       "3 16    81   INS   \n",
       "4 22   -51   DEL   \n",
       "5  7   150   INS   \n",
       "6  7    71   INS   \n",
       "  CSQ                                                                                                                                                             \n",
       "1 deletion|downstream_gene_variant|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding|||||||||||1767|-1||HGNC|KAT2B|||                \n",
       "2 insertion|intron_variant&feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||6|0.01\n",
       "3 insertion|intron_variant&feature_elongation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||2/17||||||||||-1||HGNC|KAT2B||5|0.01\n",
       "4 deletion|intron_variant&feature_truncation|MODIFIER|KAT2B|ENSBIXG00000005942|Transcript|ENSBIXT00000043470|protein_coding||1/17||||||||||-1||HGNC|KAT2B||51|0.05\n",
       "5 insertion|intron_variant&feature_elongation|MODIFIER|EFHB|ENSBIXG00000028467|Transcript|ENSBIXT00000043467|protein_coding||8/12||||||||||1||HGNC|EFHB||4|0.01   \n",
       "6 insertion|intergenic_variant|MODIFIER|||||||||||||||||||||||                                                                                                    \n",
       "  Allele    ⋯ Codons Existing_variation DISTANCE STRAND FLAGS SYMBOL_SOURCE\n",
       "1 deletion  ⋯                           1767     -1           HGNC         \n",
       "2 insertion ⋯                                    -1           HGNC         \n",
       "3 insertion ⋯                                    -1           HGNC         \n",
       "4 deletion  ⋯                                    -1           HGNC         \n",
       "5 insertion ⋯                                    1            HGNC         \n",
       "6 insertion ⋯                                                              \n",
       "  HGNC_ID HGVS_OFFSET OverlapBP OverlapPC\n",
       "1 KAT2B                         NA       \n",
       "2 KAT2B               6         0.01     \n",
       "3 KAT2B               5         0.01     \n",
       "4 KAT2B               51        0.05     \n",
       "5 EFHB                4         0.01     \n",
       "6                               NA       "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#split the annotation column (CSQ)\n",
    "t=Angus[,c(1:9)]\n",
    "head(t)\n",
    "Angus=t[, c(\"Allele\",\"Consequence\",\"IMPACT\",\"SYMBOL\",\"Gene\",\"Feature_type\",\"Feature\",\"BIOTYPE\",\"EXON\",\"INTRON\",\"HGVSc\",\"HGVSp\",\"cDNA_position\",\"CDS_position\",\"Protein_position\",\"Amino_acids\",\"Codons\",\"Existing_variation\",\"DISTANCE\",\"STRAND\",\"FLAGS\",\"SYMBOL_SOURCE\",\"HGNC_ID\",\"HGVS_OFFSET\",\"OverlapBP\",\"OverlapPC\") := tstrsplit(CSQ, \"|\", fixed=TRUE)]\n",
    "head(Angus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 6 × 9</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ID</th><th scope=col>REF</th><th scope=col>ALT</th><th scope=col>QUAL</th><th scope=col>SVLEN</th><th scope=col>SVTYPE</th><th scope=col>CSQ</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>1</td><td>162159</td><td>0</td><td>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>TTGCTCTTCTTCCCGTGCCTGATCATGCACTAATATTCTTTATCATACACTGATCGTATTTGA                                                                                                                          </td><td> 7</td><td>   71</td><td>INS</td><td>insertion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                     </td></tr>\n",
       "\t<tr><td>1</td><td>286834</td><td>1</td><td>CAGGTTGAGGACACTTTTTTTTTTTTTTTTTAGGCTTACTTGTTCAGTAAAAAAAAAAAAAAGAAAAAAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              </td><td>N                                                                                                                                                                                        </td><td>14</td><td>  -70</td><td>DEL</td><td>deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      </td></tr>\n",
       "\t<tr><td>1</td><td>383182</td><td>3</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                    </span></td><td>17</td><td>-8535</td><td>DEL</td><td><span style=white-space:pre-wrap>deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      </span></td></tr>\n",
       "\t<tr><td>1</td><td>426636</td><td>4</td><td>TGGGCCAAAGATCTAAATAGACATTTCTCCAAAGAAGACATACAGATGGCTAACAAACACATGAAAAGATGCTCAACATCACTCATTATCAGAGAAATGCAAATCAAAACCACTATGAGGTACCATTTCACACCAGTCAGAATGGCTGCGATCCAAAAGTCTACAAGCAATAAATGCTGGAGAGGGTGTGGAGAAAAGGGAACCCTCTTACACTGTTGGTGGGAATGCAAACTAGTACAGCTACTATGGAGAACAGTGTGGAGATTCCTTAAAAAACTGGAAATAGAACTGCCTTATGATCCAGCAATCCCACTGCTGGGCATACACACTGAGGAAACCAGAAGGGAAAGAGACATGTGTACCCCAATGTTCATCGCAGCACTGTTTATAATAGCCAGGACATGGAAGCAACCTAGATGTCCATCAGCAGATGAATGGATAAGAAAGCAGTGGTACATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGATTCTGTGGGAGAGGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATGTTCTATTAAAGAAAAAAAATTAAAAAAAAAATAAAATAAAGATATATTAAGTGCAAAAAAAAATTAAAAAGAAA</td><td>N                                                                                                                                                                                        </td><td> 8</td><td> -962</td><td>DEL</td><td>deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      </td></tr>\n",
       "\t<tr><td>1</td><td>438769</td><td>5</td><td>CATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGACTCTGTGGGAGATGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATTTTCTATTAAAGAAAAAAAAAGAAAAAAAAATTCAACATTCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        </td><td>N                                                                                                                                                                                        </td><td> 8</td><td> -476</td><td>DEL</td><td>deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      </td></tr>\n",
       "\t<tr><td>1</td><td>474156</td><td>6</td><td>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>TCCCTTGTCTGGGAGCATCTCGAGGGAAATCTCACCTTCCTCTTGAGCCTCGAAAGGGCACTTACACTTTGTGCAACTCAAGAAGTTCTCCGACATACCCATCTGCACTGGAGAGGAACACTGAGTTTCCTGCCACAACTCCAGAAAACCAGGAGATTCTCTCAACATGCCTGAGGGTTTAATGA</td><td> 9</td><td>  191</td><td>INS</td><td>insertion|upstream_gene_variant|MODIFIER|5S_rRNA|ENSBTAG00000047028|Transcript|ENSBTAT00000063709|rRNA|||||||||||3221|1||RFAM|||||</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 6 × 9\n",
       "\\begin{tabular}{r|lllllllll}\n",
       " CHROM & POS & ID & REF & ALT & QUAL & SVLEN & SVTYPE & CSQ\\\\\n",
       " <chr> & <int> & <chr> & <chr> & <chr> & <dbl> & <int> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t 1 & 162159 & 0 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & TTGCTCTTCTTCCCGTGCCTGATCATGCACTAATATTCTTTATCATACACTGATCGTATTTGA                                                                                                                           &  7 &    71 & INS & insertion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                     \\\\\n",
       "\t 1 & 286834 & 1 & CAGGTTGAGGACACTTTTTTTTTTTTTTTTTAGGCTTACTTGTTCAGTAAAAAAAAAAAAAAGAAAAAAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               & N                                                                                                                                                                                         & 14 &   -70 & DEL & deletion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                      \\\\\n",
       "\t 1 & 383182 & 3 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & <DEL>                                                                                                                                                                                     & 17 & -8535 & DEL & deletion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                      \\\\\n",
       "\t 1 & 426636 & 4 & TGGGCCAAAGATCTAAATAGACATTTCTCCAAAGAAGACATACAGATGGCTAACAAACACATGAAAAGATGCTCAACATCACTCATTATCAGAGAAATGCAAATCAAAACCACTATGAGGTACCATTTCACACCAGTCAGAATGGCTGCGATCCAAAAGTCTACAAGCAATAAATGCTGGAGAGGGTGTGGAGAAAAGGGAACCCTCTTACACTGTTGGTGGGAATGCAAACTAGTACAGCTACTATGGAGAACAGTGTGGAGATTCCTTAAAAAACTGGAAATAGAACTGCCTTATGATCCAGCAATCCCACTGCTGGGCATACACACTGAGGAAACCAGAAGGGAAAGAGACATGTGTACCCCAATGTTCATCGCAGCACTGTTTATAATAGCCAGGACATGGAAGCAACCTAGATGTCCATCAGCAGATGAATGGATAAGAAAGCAGTGGTACATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGATTCTGTGGGAGAGGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATGTTCTATTAAAGAAAAAAAATTAAAAAAAAAATAAAATAAAGATATATTAAGTGCAAAAAAAAATTAAAAAGAAA & N                                                                                                                                                                                         &  8 &  -962 & DEL & deletion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                      \\\\\n",
       "\t 1 & 438769 & 5 & CATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGACTCTGTGGGAGATGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATTTTCTATTAAAGAAAAAAAAAGAAAAAAAAATTCAACATTCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         & N                                                                                                                                                                                         &  8 &  -476 & DEL & deletion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                      \\\\\n",
       "\t 1 & 474156 & 6 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & TCCCTTGTCTGGGAGCATCTCGAGGGAAATCTCACCTTCCTCTTGAGCCTCGAAAGGGCACTTACACTTTGTGCAACTCAAGAAGTTCTCCGACATACCCATCTGCACTGGAGAGGAACACTGAGTTTCCTGCCACAACTCCAGAAAACCAGGAGATTCTCTCAACATGCCTGAGGGTTTAATGA &  9 &   191 & INS & insertion\\textbar{}upstream\\_gene\\_variant\\textbar{}MODIFIER\\textbar{}5S\\_rRNA\\textbar{}ENSBTAG00000047028\\textbar{}Transcript\\textbar{}ENSBTAT00000063709\\textbar{}rRNA\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}3221\\textbar{}1\\textbar{}\\textbar{}RFAM\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 6 × 9\n",
       "\n",
       "| CHROM &lt;chr&gt; | POS &lt;int&gt; | ID &lt;chr&gt; | REF &lt;chr&gt; | ALT &lt;chr&gt; | QUAL &lt;dbl&gt; | SVLEN &lt;int&gt; | SVTYPE &lt;chr&gt; | CSQ &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|\n",
       "| 1 | 162159 | 0 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | TTGCTCTTCTTCCCGTGCCTGATCATGCACTAATATTCTTTATCATACACTGATCGTATTTGA                                                                                                                           |  7 |    71 | INS | insertion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      |\n",
       "| 1 | 286834 | 1 | CAGGTTGAGGACACTTTTTTTTTTTTTTTTTAGGCTTACTTGTTCAGTAAAAAAAAAAAAAAGAAAAAAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | N                                                                                                                                                                                         | 14 |   -70 | DEL | deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                       |\n",
       "| 1 | 383182 | 3 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | &lt;DEL&gt;                                                                                                                                                                                     | 17 | -8535 | DEL | deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                       |\n",
       "| 1 | 426636 | 4 | TGGGCCAAAGATCTAAATAGACATTTCTCCAAAGAAGACATACAGATGGCTAACAAACACATGAAAAGATGCTCAACATCACTCATTATCAGAGAAATGCAAATCAAAACCACTATGAGGTACCATTTCACACCAGTCAGAATGGCTGCGATCCAAAAGTCTACAAGCAATAAATGCTGGAGAGGGTGTGGAGAAAAGGGAACCCTCTTACACTGTTGGTGGGAATGCAAACTAGTACAGCTACTATGGAGAACAGTGTGGAGATTCCTTAAAAAACTGGAAATAGAACTGCCTTATGATCCAGCAATCCCACTGCTGGGCATACACACTGAGGAAACCAGAAGGGAAAGAGACATGTGTACCCCAATGTTCATCGCAGCACTGTTTATAATAGCCAGGACATGGAAGCAACCTAGATGTCCATCAGCAGATGAATGGATAAGAAAGCAGTGGTACATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGATTCTGTGGGAGAGGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATGTTCTATTAAAGAAAAAAAATTAAAAAAAAAATAAAATAAAGATATATTAAGTGCAAAAAAAAATTAAAAAGAAA | N                                                                                                                                                                                         |  8 |  -962 | DEL | deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                       |\n",
       "| 1 | 438769 | 5 | CATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGACTCTGTGGGAGATGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATTTTCTATTAAAGAAAAAAAAAGAAAAAAAAATTCAACATTCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | N                                                                                                                                                                                         |  8 |  -476 | DEL | deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                       |\n",
       "| 1 | 474156 | 6 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | TCCCTTGTCTGGGAGCATCTCGAGGGAAATCTCACCTTCCTCTTGAGCCTCGAAAGGGCACTTACACTTTGTGCAACTCAAGAAGTTCTCCGACATACCCATCTGCACTGGAGAGGAACACTGAGTTTCCTGCCACAACTCCAGAAAACCAGGAGATTCTCTCAACATGCCTGAGGGTTTAATGA |  9 |   191 | INS | insertion|upstream_gene_variant|MODIFIER|5S_rRNA|ENSBTAG00000047028|Transcript|ENSBTAT00000063709|rRNA|||||||||||3221|1||RFAM||||| |\n",
       "\n"
      ],
      "text/plain": [
       "  CHROM POS    ID\n",
       "1 1     162159 0 \n",
       "2 1     286834 1 \n",
       "3 1     383182 3 \n",
       "4 1     426636 4 \n",
       "5 1     438769 5 \n",
       "6 1     474156 6 \n",
       "  REF                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 \n",
       "1 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "2 CAGGTTGAGGACACTTTTTTTTTTTTTTTTTAGGCTTACTTGTTCAGTAAAAAAAAAAAAAAGAAAAAAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              \n",
       "3 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "4 TGGGCCAAAGATCTAAATAGACATTTCTCCAAAGAAGACATACAGATGGCTAACAAACACATGAAAAGATGCTCAACATCACTCATTATCAGAGAAATGCAAATCAAAACCACTATGAGGTACCATTTCACACCAGTCAGAATGGCTGCGATCCAAAAGTCTACAAGCAATAAATGCTGGAGAGGGTGTGGAGAAAAGGGAACCCTCTTACACTGTTGGTGGGAATGCAAACTAGTACAGCTACTATGGAGAACAGTGTGGAGATTCCTTAAAAAACTGGAAATAGAACTGCCTTATGATCCAGCAATCCCACTGCTGGGCATACACACTGAGGAAACCAGAAGGGAAAGAGACATGTGTACCCCAATGTTCATCGCAGCACTGTTTATAATAGCCAGGACATGGAAGCAACCTAGATGTCCATCAGCAGATGAATGGATAAGAAAGCAGTGGTACATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGATTCTGTGGGAGAGGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATGTTCTATTAAAGAAAAAAAATTAAAAAAAAAATAAAATAAAGATATATTAAGTGCAAAAAAAAATTAAAAAGAAA\n",
       "5 CATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGACTCTGTGGGAGATGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATTTTCTATTAAAGAAAAAAAAAGAAAAAAAAATTCAACATTCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        \n",
       "6 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "  ALT                                                                                                                                                                                      \n",
       "1 TTGCTCTTCTTCCCGTGCCTGATCATGCACTAATATTCTTTATCATACACTGATCGTATTTGA                                                                                                                          \n",
       "2 N                                                                                                                                                                                        \n",
       "3 <DEL>                                                                                                                                                                                    \n",
       "4 N                                                                                                                                                                                        \n",
       "5 N                                                                                                                                                                                        \n",
       "6 TCCCTTGTCTGGGAGCATCTCGAGGGAAATCTCACCTTCCTCTTGAGCCTCGAAAGGGCACTTACACTTTGTGCAACTCAAGAAGTTCTCCGACATACCCATCTGCACTGGAGAGGAACACTGAGTTTCCTGCCACAACTCCAGAAAACCAGGAGATTCTCTCAACATGCCTGAGGGTTTAATGA\n",
       "  QUAL SVLEN SVTYPE\n",
       "1  7      71 INS   \n",
       "2 14     -70 DEL   \n",
       "3 17   -8535 DEL   \n",
       "4  8    -962 DEL   \n",
       "5  8    -476 DEL   \n",
       "6  9     191 INS   \n",
       "  CSQ                                                                                                                               \n",
       "1 insertion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                     \n",
       "2 deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      \n",
       "3 deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      \n",
       "4 deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      \n",
       "5 deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      \n",
       "6 insertion|upstream_gene_variant|MODIFIER|5S_rRNA|ENSBTAG00000047028|Transcript|ENSBTAT00000063709|rRNA|||||||||||3221|1||RFAM|||||"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 6 × 36</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ID</th><th scope=col>REF</th><th scope=col>ALT</th><th scope=col>QUAL</th><th scope=col>SVLEN</th><th scope=col>SVTYPE</th><th scope=col>CSQ</th><th scope=col>Allele</th><th scope=col>⋯</th><th scope=col>Existing_variation</th><th scope=col>DISTANCE</th><th scope=col>STRAND</th><th scope=col>FLAGS</th><th scope=col>SYMBOL_SOURCE</th><th scope=col>HGNC_ID</th><th scope=col>SIFT</th><th scope=col>HGVS_OFFSET</th><th scope=col>OverlapBP</th><th scope=col>OverlapPC</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;dbl&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>⋯</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>1</td><td>162159</td><td>0</td><td>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>TTGCTCTTCTTCCCGTGCCTGATCATGCACTAATATTCTTTATCATACACTGATCGTATTTGA                                                                                                                          </td><td> 7</td><td>   71</td><td>INS</td><td>insertion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                     </td><td>insertion</td><td>⋯</td><td></td><td>    </td><td> </td><td></td><td>    </td><td></td><td></td><td></td><td></td><td>NA</td></tr>\n",
       "\t<tr><td>1</td><td>286834</td><td>1</td><td>CAGGTTGAGGACACTTTTTTTTTTTTTTTTTAGGCTTACTTGTTCAGTAAAAAAAAAAAAAAGAAAAAAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              </td><td>N                                                                                                                                                                                        </td><td>14</td><td>  -70</td><td>DEL</td><td>deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      </td><td>deletion </td><td>⋯</td><td></td><td>    </td><td> </td><td></td><td>    </td><td></td><td></td><td></td><td></td><td>NA</td></tr>\n",
       "\t<tr><td>1</td><td>383182</td><td>3</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                    </span></td><td>17</td><td>-8535</td><td>DEL</td><td><span style=white-space:pre-wrap>deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      </span></td><td>deletion </td><td>⋯</td><td></td><td><span style=white-space:pre-wrap>    </span></td><td> </td><td></td><td><span style=white-space:pre-wrap>    </span></td><td></td><td></td><td></td><td></td><td>NA</td></tr>\n",
       "\t<tr><td>1</td><td>426636</td><td>4</td><td>TGGGCCAAAGATCTAAATAGACATTTCTCCAAAGAAGACATACAGATGGCTAACAAACACATGAAAAGATGCTCAACATCACTCATTATCAGAGAAATGCAAATCAAAACCACTATGAGGTACCATTTCACACCAGTCAGAATGGCTGCGATCCAAAAGTCTACAAGCAATAAATGCTGGAGAGGGTGTGGAGAAAAGGGAACCCTCTTACACTGTTGGTGGGAATGCAAACTAGTACAGCTACTATGGAGAACAGTGTGGAGATTCCTTAAAAAACTGGAAATAGAACTGCCTTATGATCCAGCAATCCCACTGCTGGGCATACACACTGAGGAAACCAGAAGGGAAAGAGACATGTGTACCCCAATGTTCATCGCAGCACTGTTTATAATAGCCAGGACATGGAAGCAACCTAGATGTCCATCAGCAGATGAATGGATAAGAAAGCAGTGGTACATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGATTCTGTGGGAGAGGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATGTTCTATTAAAGAAAAAAAATTAAAAAAAAAATAAAATAAAGATATATTAAGTGCAAAAAAAAATTAAAAAGAAA</td><td>N                                                                                                                                                                                        </td><td> 8</td><td> -962</td><td>DEL</td><td>deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      </td><td>deletion </td><td>⋯</td><td></td><td>    </td><td> </td><td></td><td>    </td><td></td><td></td><td></td><td></td><td>NA</td></tr>\n",
       "\t<tr><td>1</td><td>438769</td><td>5</td><td>CATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGACTCTGTGGGAGATGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATTTTCTATTAAAGAAAAAAAAAGAAAAAAAAATTCAACATTCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        </td><td>N                                                                                                                                                                                        </td><td> 8</td><td> -476</td><td>DEL</td><td>deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      </td><td>deletion </td><td>⋯</td><td></td><td>    </td><td> </td><td></td><td>    </td><td></td><td></td><td></td><td></td><td>NA</td></tr>\n",
       "\t<tr><td>1</td><td>474156</td><td>6</td><td>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>TCCCTTGTCTGGGAGCATCTCGAGGGAAATCTCACCTTCCTCTTGAGCCTCGAAAGGGCACTTACACTTTGTGCAACTCAAGAAGTTCTCCGACATACCCATCTGCACTGGAGAGGAACACTGAGTTTCCTGCCACAACTCCAGAAAACCAGGAGATTCTCTCAACATGCCTGAGGGTTTAATGA</td><td> 9</td><td>  191</td><td>INS</td><td>insertion|upstream_gene_variant|MODIFIER|5S_rRNA|ENSBTAG00000047028|Transcript|ENSBTAT00000063709|rRNA|||||||||||3221|1||RFAM|||||</td><td>insertion</td><td>⋯</td><td></td><td>3221</td><td>1</td><td></td><td>RFAM</td><td></td><td></td><td></td><td></td><td>NA</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 6 × 36\n",
       "\\begin{tabular}{r|llllllllllllllllllllllllllllllllllll}\n",
       " CHROM & POS & ID & REF & ALT & QUAL & SVLEN & SVTYPE & CSQ & Allele & Consequence & IMPACT & SYMBOL & Gene & Feature\\_type & Feature & BIOTYPE & EXON & INTRON & HGVSc & HGVSp & cDNA\\_position & CDS\\_position & Protein\\_position & Amino\\_acids & Codons & Existing\\_variation & DISTANCE & STRAND & FLAGS & SYMBOL\\_SOURCE & HGNC\\_ID & SIFT & HGVS\\_OFFSET & OverlapBP & OverlapPC\\\\\n",
       " <chr> & <int> & <chr> & <chr> & <chr> & <dbl> & <int> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t 1 & 162159 & 0 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & TTGCTCTTCTTCCCGTGCCTGATCATGCACTAATATTCTTTATCATACACTGATCGTATTTGA                                                                                                                           &  7 &    71 & INS & insertion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                      & insertion & intergenic\\_variant    & MODIFIER &         &                    &            &                    &      &  &  &  &  &  &  &  &  &  &  &      &   &  &      &  &  &  &  & NA\\\\\n",
       "\t 1 & 286834 & 1 & CAGGTTGAGGACACTTTTTTTTTTTTTTTTTAGGCTTACTTGTTCAGTAAAAAAAAAAAAAAGAAAAAAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               & N                                                                                                                                                                                         & 14 &   -70 & DEL & deletion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                       & deletion  & intergenic\\_variant    & MODIFIER &         &                    &            &                    &      &  &  &  &  &  &  &  &  &  &  &      &   &  &      &  &  &  &  & NA\\\\\n",
       "\t 1 & 383182 & 3 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & <DEL>                                                                                                                                                                                     & 17 & -8535 & DEL & deletion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                       & deletion  & intergenic\\_variant    & MODIFIER &         &                    &            &                    &      &  &  &  &  &  &  &  &  &  &  &      &   &  &      &  &  &  &  & NA\\\\\n",
       "\t 1 & 426636 & 4 & TGGGCCAAAGATCTAAATAGACATTTCTCCAAAGAAGACATACAGATGGCTAACAAACACATGAAAAGATGCTCAACATCACTCATTATCAGAGAAATGCAAATCAAAACCACTATGAGGTACCATTTCACACCAGTCAGAATGGCTGCGATCCAAAAGTCTACAAGCAATAAATGCTGGAGAGGGTGTGGAGAAAAGGGAACCCTCTTACACTGTTGGTGGGAATGCAAACTAGTACAGCTACTATGGAGAACAGTGTGGAGATTCCTTAAAAAACTGGAAATAGAACTGCCTTATGATCCAGCAATCCCACTGCTGGGCATACACACTGAGGAAACCAGAAGGGAAAGAGACATGTGTACCCCAATGTTCATCGCAGCACTGTTTATAATAGCCAGGACATGGAAGCAACCTAGATGTCCATCAGCAGATGAATGGATAAGAAAGCAGTGGTACATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGATTCTGTGGGAGAGGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATGTTCTATTAAAGAAAAAAAATTAAAAAAAAAATAAAATAAAGATATATTAAGTGCAAAAAAAAATTAAAAAGAAA & N                                                                                                                                                                                         &  8 &  -962 & DEL & deletion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                       & deletion  & intergenic\\_variant    & MODIFIER &         &                    &            &                    &      &  &  &  &  &  &  &  &  &  &  &      &   &  &      &  &  &  &  & NA\\\\\n",
       "\t 1 & 438769 & 5 & CATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGACTCTGTGGGAGATGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATTTTCTATTAAAGAAAAAAAAAGAAAAAAAAATTCAACATTCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         & N                                                                                                                                                                                         &  8 &  -476 & DEL & deletion\\textbar{}intergenic\\_variant\\textbar{}MODIFIER\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}                                                                       & deletion  & intergenic\\_variant    & MODIFIER &         &                    &            &                    &      &  &  &  &  &  &  &  &  &  &  &      &   &  &      &  &  &  &  & NA\\\\\n",
       "\t 1 & 474156 & 6 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & TCCCTTGTCTGGGAGCATCTCGAGGGAAATCTCACCTTCCTCTTGAGCCTCGAAAGGGCACTTACACTTTGTGCAACTCAAGAAGTTCTCCGACATACCCATCTGCACTGGAGAGGAACACTGAGTTTCCTGCCACAACTCCAGAAAACCAGGAGATTCTCTCAACATGCCTGAGGGTTTAATGA &  9 &   191 & INS & insertion\\textbar{}upstream\\_gene\\_variant\\textbar{}MODIFIER\\textbar{}5S\\_rRNA\\textbar{}ENSBTAG00000047028\\textbar{}Transcript\\textbar{}ENSBTAT00000063709\\textbar{}rRNA\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{}3221\\textbar{}1\\textbar{}\\textbar{}RFAM\\textbar{}\\textbar{}\\textbar{}\\textbar{}\\textbar{} & insertion & upstream\\_gene\\_variant & MODIFIER & 5S\\_rRNA & ENSBTAG00000047028 & Transcript & ENSBTAT00000063709 & rRNA &  &  &  &  &  &  &  &  &  &  & 3221 & 1 &  & RFAM &  &  &  &  & NA\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 6 × 36\n",
       "\n",
       "| CHROM &lt;chr&gt; | POS &lt;int&gt; | ID &lt;chr&gt; | REF &lt;chr&gt; | ALT &lt;chr&gt; | QUAL &lt;dbl&gt; | SVLEN &lt;int&gt; | SVTYPE &lt;chr&gt; | CSQ &lt;chr&gt; | Allele &lt;chr&gt; | ⋯ ⋯ | Existing_variation &lt;chr&gt; | DISTANCE &lt;chr&gt; | STRAND &lt;chr&gt; | FLAGS &lt;chr&gt; | SYMBOL_SOURCE &lt;chr&gt; | HGNC_ID &lt;chr&gt; | SIFT &lt;chr&gt; | HGVS_OFFSET &lt;chr&gt; | OverlapBP &lt;chr&gt; | OverlapPC &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| 1 | 162159 | 0 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | TTGCTCTTCTTCCCGTGCCTGATCATGCACTAATATTCTTTATCATACACTGATCGTATTTGA                                                                                                                           |  7 |    71 | INS | insertion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      | insertion | ⋯ | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | NA |\n",
       "| 1 | 286834 | 1 | CAGGTTGAGGACACTTTTTTTTTTTTTTTTTAGGCTTACTTGTTCAGTAAAAAAAAAAAAAAGAAAAAAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | N                                                                                                                                                                                         | 14 |   -70 | DEL | deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                       | deletion  | ⋯ | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | NA |\n",
       "| 1 | 383182 | 3 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | &lt;DEL&gt;                                                                                                                                                                                     | 17 | -8535 | DEL | deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                       | deletion  | ⋯ | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | NA |\n",
       "| 1 | 426636 | 4 | TGGGCCAAAGATCTAAATAGACATTTCTCCAAAGAAGACATACAGATGGCTAACAAACACATGAAAAGATGCTCAACATCACTCATTATCAGAGAAATGCAAATCAAAACCACTATGAGGTACCATTTCACACCAGTCAGAATGGCTGCGATCCAAAAGTCTACAAGCAATAAATGCTGGAGAGGGTGTGGAGAAAAGGGAACCCTCTTACACTGTTGGTGGGAATGCAAACTAGTACAGCTACTATGGAGAACAGTGTGGAGATTCCTTAAAAAACTGGAAATAGAACTGCCTTATGATCCAGCAATCCCACTGCTGGGCATACACACTGAGGAAACCAGAAGGGAAAGAGACATGTGTACCCCAATGTTCATCGCAGCACTGTTTATAATAGCCAGGACATGGAAGCAACCTAGATGTCCATCAGCAGATGAATGGATAAGAAAGCAGTGGTACATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGATTCTGTGGGAGAGGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATGTTCTATTAAAGAAAAAAAATTAAAAAAAAAATAAAATAAAGATATATTAAGTGCAAAAAAAAATTAAAAAGAAA | N                                                                                                                                                                                         |  8 |  -962 | DEL | deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                       | deletion  | ⋯ | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | NA |\n",
       "| 1 | 438769 | 5 | CATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGACTCTGTGGGAGATGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATTTTCTATTAAAGAAAAAAAAAGAAAAAAAAATTCAACATTCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | N                                                                                                                                                                                         |  8 |  -476 | DEL | deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                       | deletion  | ⋯ | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | <!----> | NA |\n",
       "| 1 | 474156 | 6 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | TCCCTTGTCTGGGAGCATCTCGAGGGAAATCTCACCTTCCTCTTGAGCCTCGAAAGGGCACTTACACTTTGTGCAACTCAAGAAGTTCTCCGACATACCCATCTGCACTGGAGAGGAACACTGAGTTTCCTGCCACAACTCCAGAAAACCAGGAGATTCTCTCAACATGCCTGAGGGTTTAATGA |  9 |   191 | INS | insertion|upstream_gene_variant|MODIFIER|5S_rRNA|ENSBTAG00000047028|Transcript|ENSBTAT00000063709|rRNA|||||||||||3221|1||RFAM||||| | insertion | ⋯ | <!----> | 3221 | 1 | <!----> | RFAM | <!----> | <!----> | <!----> | <!----> | NA |\n",
       "\n"
      ],
      "text/plain": [
       "  CHROM POS    ID\n",
       "1 1     162159 0 \n",
       "2 1     286834 1 \n",
       "3 1     383182 3 \n",
       "4 1     426636 4 \n",
       "5 1     438769 5 \n",
       "6 1     474156 6 \n",
       "  REF                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 \n",
       "1 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "2 CAGGTTGAGGACACTTTTTTTTTTTTTTTTTAGGCTTACTTGTTCAGTAAAAAAAAAAAAAAGAAAAAAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              \n",
       "3 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "4 TGGGCCAAAGATCTAAATAGACATTTCTCCAAAGAAGACATACAGATGGCTAACAAACACATGAAAAGATGCTCAACATCACTCATTATCAGAGAAATGCAAATCAAAACCACTATGAGGTACCATTTCACACCAGTCAGAATGGCTGCGATCCAAAAGTCTACAAGCAATAAATGCTGGAGAGGGTGTGGAGAAAAGGGAACCCTCTTACACTGTTGGTGGGAATGCAAACTAGTACAGCTACTATGGAGAACAGTGTGGAGATTCCTTAAAAAACTGGAAATAGAACTGCCTTATGATCCAGCAATCCCACTGCTGGGCATACACACTGAGGAAACCAGAAGGGAAAGAGACATGTGTACCCCAATGTTCATCGCAGCACTGTTTATAATAGCCAGGACATGGAAGCAACCTAGATGTCCATCAGCAGATGAATGGATAAGAAAGCAGTGGTACATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGATTCTGTGGGAGAGGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATGTTCTATTAAAGAAAAAAAATTAAAAAAAAAATAAAATAAAGATATATTAAGTGCAAAAAAAAATTAAAAAGAAA\n",
       "5 CATATACACAATGGAGTATTACTCAGCCATTAAAAAGAATACATTTGAATCAGTTCTAATGAGGTGGATGAAACTGGAGCCTATTATACAGAGTGAAGTAAGCCAGAAGGAAAAACACCAATACAGTATACTAACGCATATATATGGAATTTAGAAAGATGGTAACGATAACCCTGTATACGAGACAGCAAAAGAGACACTGATGTATAGAACAGTCTTATGGACTCTGTGGGAGATGGAGAGGGTGGGAAGATTTGGGAGAATGGCATTGAAACATGTGAAACGTCATGTATGAAACGAGATGCCAGTCCAGGTTCAATGCACGATGCTGGATGCTTGGGGCTGGTGCACTGGGACGACCCAGAGGGATGGTGTGGGGAGGGAGGAGGGAGGAGGGTTCAGGATGGGGAACACATGTATACTAATTAAATAATTTTCTATTAAAGAAAAAAAAAGAAAAAAAAATTCAACATTCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        \n",
       "6 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "  ALT                                                                                                                                                                                      \n",
       "1 TTGCTCTTCTTCCCGTGCCTGATCATGCACTAATATTCTTTATCATACACTGATCGTATTTGA                                                                                                                          \n",
       "2 N                                                                                                                                                                                        \n",
       "3 <DEL>                                                                                                                                                                                    \n",
       "4 N                                                                                                                                                                                        \n",
       "5 N                                                                                                                                                                                        \n",
       "6 TCCCTTGTCTGGGAGCATCTCGAGGGAAATCTCACCTTCCTCTTGAGCCTCGAAAGGGCACTTACACTTTGTGCAACTCAAGAAGTTCTCCGACATACCCATCTGCACTGGAGAGGAACACTGAGTTTCCTGCCACAACTCCAGAAAACCAGGAGATTCTCTCAACATGCCTGAGGGTTTAATGA\n",
       "  QUAL SVLEN SVTYPE\n",
       "1  7      71 INS   \n",
       "2 14     -70 DEL   \n",
       "3 17   -8535 DEL   \n",
       "4  8    -962 DEL   \n",
       "5  8    -476 DEL   \n",
       "6  9     191 INS   \n",
       "  CSQ                                                                                                                               \n",
       "1 insertion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                     \n",
       "2 deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      \n",
       "3 deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      \n",
       "4 deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      \n",
       "5 deletion|intergenic_variant|MODIFIER||||||||||||||||||||||||                                                                      \n",
       "6 insertion|upstream_gene_variant|MODIFIER|5S_rRNA|ENSBTAG00000047028|Transcript|ENSBTAT00000063709|rRNA|||||||||||3221|1||RFAM|||||\n",
       "  Allele    ⋯ Existing_variation DISTANCE STRAND FLAGS SYMBOL_SOURCE HGNC_ID\n",
       "1 insertion ⋯                                                               \n",
       "2 deletion  ⋯                                                               \n",
       "3 deletion  ⋯                                                               \n",
       "4 deletion  ⋯                                                               \n",
       "5 deletion  ⋯                                                               \n",
       "6 insertion ⋯                    3221     1            RFAM                 \n",
       "  SIFT HGVS_OFFSET OverlapBP OverlapPC\n",
       "1                            NA       \n",
       "2                            NA       \n",
       "3                            NA       \n",
       "4                            NA       \n",
       "5                            NA       \n",
       "6                            NA       "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#split the annotation column (CSQ)\n",
    "\n",
    "a=UCD[,c(1:9)]\n",
    "head(a)\n",
    "UCD=a[, c(\"Allele\",\"Consequence\",\"IMPACT\",\"SYMBOL\",\"Gene\",\"Feature_type\",\"Feature\",\"BIOTYPE\",\"EXON\",\"INTRON\",\"HGVSc\",\"HGVSp\",\"cDNA_position\",\"CDS_position\",\"Protein_position\",\"Amino_acids\",\"Codons\",\"Existing_variation\",\"DISTANCE\",\"STRAND\",\"FLAGS\",\"SYMBOL_SOURCE\",\"HGNC_ID\",\"SIFT\",\"HGVS_OFFSET\",\"OverlapBP\",\"OverlapPC\") := tstrsplit(CSQ, \"|\", fixed=TRUE)]\n",
    "head(UCD)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "#keep only the variants that are on autosomes (chr1:29)\n",
    "auto_angus=Angus[CHROM!='Y']\n",
    "auto_UCD=UCD[CHROM!='X']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 3 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>IMPACT</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>MODIFIER</td><td>13208</td></tr>\n",
       "\t<tr><td>HIGH    </td><td>   82</td></tr>\n",
       "\t<tr><td>MODERATE</td><td>    5</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 3 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " IMPACT & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t MODIFIER & 13208\\\\\n",
       "\t HIGH     &    82\\\\\n",
       "\t MODERATE &     5\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 3 × 2\n",
       "\n",
       "| IMPACT &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| MODIFIER | 13208 |\n",
       "| HIGH     |    82 |\n",
       "| MODERATE |     5 |\n",
       "\n"
      ],
      "text/plain": [
       "  IMPACT   N    \n",
       "1 MODIFIER 13208\n",
       "2 HIGH        82\n",
       "3 MODERATE     5"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 3 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>IMPACT</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>MODIFIER</td><td>12968</td></tr>\n",
       "\t<tr><td>HIGH    </td><td>   79</td></tr>\n",
       "\t<tr><td>MODERATE</td><td>    5</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 3 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " IMPACT & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t MODIFIER & 12968\\\\\n",
       "\t HIGH     &    79\\\\\n",
       "\t MODERATE &     5\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 3 × 2\n",
       "\n",
       "| IMPACT &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| MODIFIER | 12968 |\n",
       "| HIGH     |    79 |\n",
       "| MODERATE |     5 |\n",
       "\n"
      ],
      "text/plain": [
       "  IMPACT   N    \n",
       "1 MODIFIER 12968\n",
       "2 HIGH        79\n",
       "3 MODERATE     5"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 3 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>IMPACT</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>MODIFIER</td><td>12496</td></tr>\n",
       "\t<tr><td>HIGH    </td><td>   74</td></tr>\n",
       "\t<tr><td>MODERATE</td><td>    2</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 3 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " IMPACT & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t MODIFIER & 12496\\\\\n",
       "\t HIGH     &    74\\\\\n",
       "\t MODERATE &     2\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 3 × 2\n",
       "\n",
       "| IMPACT &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| MODIFIER | 12496 |\n",
       "| HIGH     |    74 |\n",
       "| MODERATE |     2 |\n",
       "\n"
      ],
      "text/plain": [
       "  IMPACT   N    \n",
       "1 MODIFIER 12496\n",
       "2 HIGH        74\n",
       "3 MODERATE     2"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 3 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>IMPACT</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>MODIFIER</td><td>12469</td></tr>\n",
       "\t<tr><td>HIGH    </td><td>   74</td></tr>\n",
       "\t<tr><td>MODERATE</td><td>    2</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 3 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " IMPACT & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t MODIFIER & 12469\\\\\n",
       "\t HIGH     &    74\\\\\n",
       "\t MODERATE &     2\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 3 × 2\n",
       "\n",
       "| IMPACT &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| MODIFIER | 12469 |\n",
       "| HIGH     |    74 |\n",
       "| MODERATE |     2 |\n",
       "\n"
      ],
      "text/plain": [
       "  IMPACT   N    \n",
       "1 MODIFIER 12469\n",
       "2 HIGH        74\n",
       "3 MODERATE     2"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#summarize the SV by the predicted impact\n",
    "\n",
    "UCD[, .(.N), by = .(IMPACT)]\n",
    "auto_UCD[, .(.N), by = .(IMPACT)]\n",
    "Angus[, .(.N), by = .(IMPACT)]\n",
    "auto_angus[, .(.N), by = .(IMPACT)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 5 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SVTYPE</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>INS</td><td>5465</td></tr>\n",
       "\t<tr><td>DEL</td><td>7465</td></tr>\n",
       "\t<tr><td>DUP</td><td> 323</td></tr>\n",
       "\t<tr><td>TRA</td><td>  22</td></tr>\n",
       "\t<tr><td>INV</td><td>  20</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 5 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " SVTYPE & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t INS & 5465\\\\\n",
       "\t DEL & 7465\\\\\n",
       "\t DUP &  323\\\\\n",
       "\t TRA &   22\\\\\n",
       "\t INV &   20\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 5 × 2\n",
       "\n",
       "| SVTYPE &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| INS | 5465 |\n",
       "| DEL | 7465 |\n",
       "| DUP |  323 |\n",
       "| TRA |   22 |\n",
       "| INV |   20 |\n",
       "\n"
      ],
      "text/plain": [
       "  SVTYPE N   \n",
       "1 INS    5465\n",
       "2 DEL    7465\n",
       "3 DUP     323\n",
       "4 TRA      22\n",
       "5 INV      20"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 5 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SVTYPE</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>DEL</td><td>7228</td></tr>\n",
       "\t<tr><td>INS</td><td>4998</td></tr>\n",
       "\t<tr><td>DUP</td><td> 323</td></tr>\n",
       "\t<tr><td>INV</td><td>  10</td></tr>\n",
       "\t<tr><td>TRA</td><td>  13</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 5 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " SVTYPE & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t DEL & 7228\\\\\n",
       "\t INS & 4998\\\\\n",
       "\t DUP &  323\\\\\n",
       "\t INV &   10\\\\\n",
       "\t TRA &   13\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 5 × 2\n",
       "\n",
       "| SVTYPE &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| DEL | 7228 |\n",
       "| INS | 4998 |\n",
       "| DUP |  323 |\n",
       "| INV |   10 |\n",
       "| TRA |   13 |\n",
       "\n"
      ],
      "text/plain": [
       "  SVTYPE N   \n",
       "1 DEL    7228\n",
       "2 INS    4998\n",
       "3 DUP     323\n",
       "4 INV      10\n",
       "5 TRA      13"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 5 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SVTYPE</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>DEL</td><td>7210</td></tr>\n",
       "\t<tr><td>INS</td><td>4992</td></tr>\n",
       "\t<tr><td>DUP</td><td> 320</td></tr>\n",
       "\t<tr><td>INV</td><td>  10</td></tr>\n",
       "\t<tr><td>TRA</td><td>  13</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 5 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " SVTYPE & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t DEL & 7210\\\\\n",
       "\t INS & 4992\\\\\n",
       "\t DUP &  320\\\\\n",
       "\t INV &   10\\\\\n",
       "\t TRA &   13\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 5 × 2\n",
       "\n",
       "| SVTYPE &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| DEL | 7210 |\n",
       "| INS | 4992 |\n",
       "| DUP |  320 |\n",
       "| INV |   10 |\n",
       "| TRA |   13 |\n",
       "\n"
      ],
      "text/plain": [
       "  SVTYPE N   \n",
       "1 DEL    7210\n",
       "2 INS    4992\n",
       "3 DUP     320\n",
       "4 INV      10\n",
       "5 TRA      13"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 5 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SVTYPE</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>INS</td><td>5388</td></tr>\n",
       "\t<tr><td>DEL</td><td>7308</td></tr>\n",
       "\t<tr><td>DUP</td><td> 317</td></tr>\n",
       "\t<tr><td>TRA</td><td>  22</td></tr>\n",
       "\t<tr><td>INV</td><td>  17</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 5 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " SVTYPE & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t INS & 5388\\\\\n",
       "\t DEL & 7308\\\\\n",
       "\t DUP &  317\\\\\n",
       "\t TRA &   22\\\\\n",
       "\t INV &   17\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 5 × 2\n",
       "\n",
       "| SVTYPE &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| INS | 5388 |\n",
       "| DEL | 7308 |\n",
       "| DUP |  317 |\n",
       "| TRA |   22 |\n",
       "| INV |   17 |\n",
       "\n"
      ],
      "text/plain": [
       "  SVTYPE N   \n",
       "1 INS    5388\n",
       "2 DEL    7308\n",
       "3 DUP     317\n",
       "4 TRA      22\n",
       "5 INV      17"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#summarize the SV by the types\n",
    "\n",
    "UCD[, .(.N), by = .(SVTYPE)]\n",
    "Angus[, .(.N), by = .(SVTYPE)]\n",
    "auto_angus[, .(.N), by = .(SVTYPE)]\n",
    "auto_UCD[, .(.N), by = .(SVTYPE)]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 36 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>Consequence</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>downstream_gene_variant                                                                                    </td><td> 546</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                                                                          </span></td><td>1841</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>intron_variant&amp;feature_truncation                                                                          </span></td><td>2582</td></tr>\n",
       "\t<tr><td>intergenic_variant                                                                                         </td><td>6480</td></tr>\n",
       "\t<tr><td>upstream_gene_variant                                                                                      </td><td> 504</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation                                            </span></td><td> 169</td></tr>\n",
       "\t<tr><td>transcript_ablation                                                                                        </td><td>  51</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>intron_variant&amp;non_coding_transcript_variant&amp;feature_truncation                                            </span></td><td> 243</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>3_prime_UTR_variant&amp;feature_elongation                                                                     </span></td><td><span style=white-space:pre-wrap>  12</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                                                      </span></td><td><span style=white-space:pre-wrap>   4</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>non_coding_transcript_exon_variant&amp;feature_truncation                                                      </span></td><td><span style=white-space:pre-wrap>  15</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>5_prime_UTR_variant&amp;feature_truncation                                                                     </span></td><td><span style=white-space:pre-wrap>   6</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                   </span></td><td><span style=white-space:pre-wrap>   3</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                             </span></td><td><span style=white-space:pre-wrap>   2</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                              </span></td><td><span style=white-space:pre-wrap>   4</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>3_prime_UTR_variant&amp;feature_truncation                                                                     </span></td><td><span style=white-space:pre-wrap>  11</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                                      </span></td><td><span style=white-space:pre-wrap>   8</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>inframe_deletion&amp;feature_truncation                                                                        </span></td><td><span style=white-space:pre-wrap>   2</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>non_coding_transcript_exon_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td><span style=white-space:pre-wrap>   8</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>5_prime_UTR_variant&amp;feature_elongation                                                                     </span></td><td><span style=white-space:pre-wrap>   4</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>non_coding_transcript_variant&amp;feature_elongation                                                           </span></td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td><span style=white-space:pre-wrap>   9</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                                 </span></td><td><span style=white-space:pre-wrap>   2</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td><td><span style=white-space:pre-wrap>   7</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant                                                 </span></td><td><span style=white-space:pre-wrap>   2</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>non_coding_transcript_exon_variant&amp;feature_elongation                                                      </span></td><td><span style=white-space:pre-wrap>   9</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                                 </span></td><td><span style=white-space:pre-wrap>   7</span></td></tr>\n",
       "\t<tr><td>non_coding_transcript_exon_variant                                                                         </td><td>   1</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                                  </span></td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "\t<tr><td>3_prime_UTR_variant                                                                                        </td><td>   1</td></tr>\n",
       "\t<tr><td>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation</td><td><span style=white-space:pre-wrap>   3</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                                                      </span></td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant                             </span></td><td><span style=white-space:pre-wrap>   2</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation               </span></td><td><span style=white-space:pre-wrap>   2</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;3_prime_UTR_variant                                                                </span></td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "\t<tr><td>intron_variant                                                                                             </td><td>   1</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 36 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " Consequence & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t downstream\\_gene\\_variant                                                                                     &  546\\\\\n",
       "\t intron\\_variant\\&feature\\_elongation                                                                           & 1841\\\\\n",
       "\t intron\\_variant\\&feature\\_truncation                                                                           & 2582\\\\\n",
       "\t intergenic\\_variant                                                                                          & 6480\\\\\n",
       "\t upstream\\_gene\\_variant                                                                                       &  504\\\\\n",
       "\t intron\\_variant\\&non\\_coding\\_transcript\\_variant\\&feature\\_elongation                                             &  169\\\\\n",
       "\t transcript\\_ablation                                                                                         &   51\\\\\n",
       "\t intron\\_variant\\&non\\_coding\\_transcript\\_variant\\&feature\\_truncation                                             &  243\\\\\n",
       "\t 3\\_prime\\_UTR\\_variant\\&feature\\_elongation                                                                      &   12\\\\\n",
       "\t 3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                                                       &    4\\\\\n",
       "\t non\\_coding\\_transcript\\_exon\\_variant\\&feature\\_truncation                                                       &   15\\\\\n",
       "\t 5\\_prime\\_UTR\\_variant\\&feature\\_truncation                                                                      &    6\\\\\n",
       "\t stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                                    &    3\\\\\n",
       "\t coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&feature\\_truncation                                              &    2\\\\\n",
       "\t coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                               &    4\\\\\n",
       "\t 3\\_prime\\_UTR\\_variant\\&feature\\_truncation                                                                      &   11\\\\\n",
       "\t frameshift\\_variant\\&feature\\_truncation                                                                       &    8\\\\\n",
       "\t inframe\\_deletion\\&feature\\_truncation                                                                         &    2\\\\\n",
       "\t non\\_coding\\_transcript\\_exon\\_variant\\&intron\\_variant\\&feature\\_truncation                                        &    8\\\\\n",
       "\t 5\\_prime\\_UTR\\_variant\\&feature\\_elongation                                                                      &    4\\\\\n",
       "\t non\\_coding\\_transcript\\_variant\\&feature\\_elongation                                                            &    1\\\\\n",
       "\t coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   &    9\\\\\n",
       "\t coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant                                                  &    2\\\\\n",
       "\t stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                     &    7\\\\\n",
       "\t coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant                                                  &    2\\\\\n",
       "\t non\\_coding\\_transcript\\_exon\\_variant\\&feature\\_elongation                                                       &    9\\\\\n",
       "\t coding\\_sequence\\_variant\\&feature\\_elongation                                                                  &    7\\\\\n",
       "\t non\\_coding\\_transcript\\_exon\\_variant                                                                          &    1\\\\\n",
       "\t coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_elongation                                                   &    1\\\\\n",
       "\t 3\\_prime\\_UTR\\_variant                                                                                         &    1\\\\\n",
       "\t stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation &    3\\\\\n",
       "\t 5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                                                       &    1\\\\\n",
       "\t coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant                              &    2\\\\\n",
       "\t stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                &    2\\\\\n",
       "\t coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant                                                                 &    1\\\\\n",
       "\t intron\\_variant                                                                                              &    1\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 36 × 2\n",
       "\n",
       "| Consequence &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| downstream_gene_variant                                                                                     |  546 |\n",
       "| intron_variant&amp;feature_elongation                                                                           | 1841 |\n",
       "| intron_variant&amp;feature_truncation                                                                           | 2582 |\n",
       "| intergenic_variant                                                                                          | 6480 |\n",
       "| upstream_gene_variant                                                                                       |  504 |\n",
       "| intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation                                             |  169 |\n",
       "| transcript_ablation                                                                                         |   51 |\n",
       "| intron_variant&amp;non_coding_transcript_variant&amp;feature_truncation                                             |  243 |\n",
       "| 3_prime_UTR_variant&amp;feature_elongation                                                                      |   12 |\n",
       "| 3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                                                       |    4 |\n",
       "| non_coding_transcript_exon_variant&amp;feature_truncation                                                       |   15 |\n",
       "| 5_prime_UTR_variant&amp;feature_truncation                                                                      |    6 |\n",
       "| stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                    |    3 |\n",
       "| coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                              |    2 |\n",
       "| coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                               |    4 |\n",
       "| 3_prime_UTR_variant&amp;feature_truncation                                                                      |   11 |\n",
       "| frameshift_variant&amp;feature_truncation                                                                       |    8 |\n",
       "| inframe_deletion&amp;feature_truncation                                                                         |    2 |\n",
       "| non_coding_transcript_exon_variant&amp;intron_variant&amp;feature_truncation                                        |    8 |\n",
       "| 5_prime_UTR_variant&amp;feature_elongation                                                                      |    4 |\n",
       "| non_coding_transcript_variant&amp;feature_elongation                                                            |    1 |\n",
       "| coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   |    9 |\n",
       "| coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                                  |    2 |\n",
       "| stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     |    7 |\n",
       "| coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant                                                  |    2 |\n",
       "| non_coding_transcript_exon_variant&amp;feature_elongation                                                       |    9 |\n",
       "| coding_sequence_variant&amp;feature_elongation                                                                  |    7 |\n",
       "| non_coding_transcript_exon_variant                                                                          |    1 |\n",
       "| coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                                   |    1 |\n",
       "| 3_prime_UTR_variant                                                                                         |    1 |\n",
       "| stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation |    3 |\n",
       "| 5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                                                       |    1 |\n",
       "| coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant                              |    2 |\n",
       "| stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation                |    2 |\n",
       "| coding_sequence_variant&amp;3_prime_UTR_variant                                                                 |    1 |\n",
       "| intron_variant                                                                                              |    1 |\n",
       "\n"
      ],
      "text/plain": [
       "   Consequence                                                                                                \n",
       "1  downstream_gene_variant                                                                                    \n",
       "2  intron_variant&feature_elongation                                                                          \n",
       "3  intron_variant&feature_truncation                                                                          \n",
       "4  intergenic_variant                                                                                         \n",
       "5  upstream_gene_variant                                                                                      \n",
       "6  intron_variant&non_coding_transcript_variant&feature_elongation                                            \n",
       "7  transcript_ablation                                                                                        \n",
       "8  intron_variant&non_coding_transcript_variant&feature_truncation                                            \n",
       "9  3_prime_UTR_variant&feature_elongation                                                                     \n",
       "10 3_prime_UTR_variant&intron_variant&feature_truncation                                                      \n",
       "11 non_coding_transcript_exon_variant&feature_truncation                                                      \n",
       "12 5_prime_UTR_variant&feature_truncation                                                                     \n",
       "13 stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                                   \n",
       "14 coding_sequence_variant&5_prime_UTR_variant&feature_truncation                                             \n",
       "15 coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation                              \n",
       "16 3_prime_UTR_variant&feature_truncation                                                                     \n",
       "17 frameshift_variant&feature_truncation                                                                      \n",
       "18 inframe_deletion&feature_truncation                                                                        \n",
       "19 non_coding_transcript_exon_variant&intron_variant&feature_truncation                                       \n",
       "20 5_prime_UTR_variant&feature_elongation                                                                     \n",
       "21 non_coding_transcript_variant&feature_elongation                                                           \n",
       "22 coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "23 coding_sequence_variant&5_prime_UTR_variant&intron_variant                                                 \n",
       "24 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "25 coding_sequence_variant&3_prime_UTR_variant&intron_variant                                                 \n",
       "26 non_coding_transcript_exon_variant&feature_elongation                                                      \n",
       "27 coding_sequence_variant&feature_elongation                                                                 \n",
       "28 non_coding_transcript_exon_variant                                                                         \n",
       "29 coding_sequence_variant&intron_variant&feature_elongation                                                  \n",
       "30 3_prime_UTR_variant                                                                                        \n",
       "31 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant&feature_truncation\n",
       "32 5_prime_UTR_variant&intron_variant&feature_truncation                                                      \n",
       "33 coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant                             \n",
       "34 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation               \n",
       "35 coding_sequence_variant&3_prime_UTR_variant                                                                \n",
       "36 intron_variant                                                                                             \n",
       "   N   \n",
       "1   546\n",
       "2  1841\n",
       "3  2582\n",
       "4  6480\n",
       "5   504\n",
       "6   169\n",
       "7    51\n",
       "8   243\n",
       "9    12\n",
       "10    4\n",
       "11   15\n",
       "12    6\n",
       "13    3\n",
       "14    2\n",
       "15    4\n",
       "16   11\n",
       "17    8\n",
       "18    2\n",
       "19    8\n",
       "20    4\n",
       "21    1\n",
       "22    9\n",
       "23    2\n",
       "24    7\n",
       "25    2\n",
       "26    9\n",
       "27    7\n",
       "28    1\n",
       "29    1\n",
       "30    1\n",
       "31    3\n",
       "32    1\n",
       "33    2\n",
       "34    2\n",
       "35    1\n",
       "36    1"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 31 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>Consequence</th><th scope=col>N</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>intergenic_variant                                                                              </td><td>7983</td></tr>\n",
       "\t<tr><td>upstream_gene_variant                                                                           </td><td> 492</td></tr>\n",
       "\t<tr><td>downstream_gene_variant                                                                         </td><td> 505</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>intron_variant&amp;feature_truncation                                                               </span></td><td>2182</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                                                               </span></td><td>1613</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                      </span></td><td><span style=white-space:pre-wrap>   5</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation                                 </span></td><td><span style=white-space:pre-wrap>  55</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>intron_variant&amp;non_coding_transcript_variant&amp;feature_truncation                                 </span></td><td><span style=white-space:pre-wrap>  76</span></td></tr>\n",
       "\t<tr><td>transcript_ablation                                                                             </td><td>  62</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>5_prime_UTR_variant&amp;feature_elongation                                                          </span></td><td><span style=white-space:pre-wrap>   5</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>3_prime_UTR_variant&amp;feature_elongation                                                          </span></td><td><span style=white-space:pre-wrap>   4</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td><span style=white-space:pre-wrap>  12</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>5_prime_UTR_variant&amp;feature_truncation                                                          </span></td><td><span style=white-space:pre-wrap>   2</span></td></tr>\n",
       "\t<tr><td>transcript_amplification                                                                        </td><td>   5</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                      </span></td><td><span style=white-space:pre-wrap>   7</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                  </span></td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                   </span></td><td><span style=white-space:pre-wrap>   3</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                           </span></td><td><span style=white-space:pre-wrap>   5</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>inframe_deletion&amp;feature_truncation                                                             </span></td><td><span style=white-space:pre-wrap>   5</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>non_coding_transcript_exon_variant&amp;feature_truncation                                           </span></td><td><span style=white-space:pre-wrap>   8</span></td></tr>\n",
       "\t<tr><td>intron_variant                                                                                  </td><td>   1</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation    </span></td><td><span style=white-space:pre-wrap>   2</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>3_prime_UTR_variant&amp;feature_truncation                                                          </span></td><td><span style=white-space:pre-wrap>   5</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                       </span></td><td><span style=white-space:pre-wrap>   2</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>non_coding_transcript_exon_variant&amp;feature_elongation                                           </span></td><td><span style=white-space:pre-wrap>   4</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation         </span></td><td><span style=white-space:pre-wrap>   3</span></td></tr>\n",
       "\t<tr><td>start_lost&amp;start_retained_variant&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation</td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>non_coding_transcript_exon_variant&amp;intron_variant&amp;feature_elongation                            </span></td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                                           </span></td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                        </span></td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>non_coding_transcript_exon_variant&amp;intron_variant&amp;feature_truncation                            </span></td><td><span style=white-space:pre-wrap>   1</span></td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 31 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " Consequence & N\\\\\n",
       " <chr> & <int>\\\\\n",
       "\\hline\n",
       "\t intergenic\\_variant                                                                               & 7983\\\\\n",
       "\t upstream\\_gene\\_variant                                                                            &  492\\\\\n",
       "\t downstream\\_gene\\_variant                                                                          &  505\\\\\n",
       "\t intron\\_variant\\&feature\\_truncation                                                                & 2182\\\\\n",
       "\t intron\\_variant\\&feature\\_elongation                                                                & 1613\\\\\n",
       "\t coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant                                       &    5\\\\\n",
       "\t intron\\_variant\\&non\\_coding\\_transcript\\_variant\\&feature\\_elongation                                  &   55\\\\\n",
       "\t intron\\_variant\\&non\\_coding\\_transcript\\_variant\\&feature\\_truncation                                  &   76\\\\\n",
       "\t transcript\\_ablation                                                                              &   62\\\\\n",
       "\t 5\\_prime\\_UTR\\_variant\\&feature\\_elongation                                                           &    5\\\\\n",
       "\t 3\\_prime\\_UTR\\_variant\\&feature\\_elongation                                                           &    4\\\\\n",
       "\t coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        &   12\\\\\n",
       "\t 5\\_prime\\_UTR\\_variant\\&feature\\_truncation                                                           &    2\\\\\n",
       "\t transcript\\_amplification                                                                         &    5\\\\\n",
       "\t coding\\_sequence\\_variant\\&feature\\_elongation                                                       &    7\\\\\n",
       "\t coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&feature\\_truncation                                   &    1\\\\\n",
       "\t coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    &    3\\\\\n",
       "\t frameshift\\_variant\\&feature\\_truncation                                                            &    5\\\\\n",
       "\t inframe\\_deletion\\&feature\\_truncation                                                              &    5\\\\\n",
       "\t non\\_coding\\_transcript\\_exon\\_variant\\&feature\\_truncation                                            &    8\\\\\n",
       "\t intron\\_variant                                                                                   &    1\\\\\n",
       "\t stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation     &    2\\\\\n",
       "\t 3\\_prime\\_UTR\\_variant\\&feature\\_truncation                                                           &    5\\\\\n",
       "\t coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_elongation                                        &    2\\\\\n",
       "\t non\\_coding\\_transcript\\_exon\\_variant\\&feature\\_elongation                                            &    4\\\\\n",
       "\t stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation          &    3\\\\\n",
       "\t start\\_lost\\&start\\_retained\\_variant\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&feature\\_truncation &    1\\\\\n",
       "\t non\\_coding\\_transcript\\_exon\\_variant\\&intron\\_variant\\&feature\\_elongation                             &    1\\\\\n",
       "\t 3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                                            &    1\\\\\n",
       "\t stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                         &    1\\\\\n",
       "\t non\\_coding\\_transcript\\_exon\\_variant\\&intron\\_variant\\&feature\\_truncation                             &    1\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 31 × 2\n",
       "\n",
       "| Consequence &lt;chr&gt; | N &lt;int&gt; |\n",
       "|---|---|\n",
       "| intergenic_variant                                                                               | 7983 |\n",
       "| upstream_gene_variant                                                                            |  492 |\n",
       "| downstream_gene_variant                                                                          |  505 |\n",
       "| intron_variant&amp;feature_truncation                                                                | 2182 |\n",
       "| intron_variant&amp;feature_elongation                                                                | 1613 |\n",
       "| coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                       |    5 |\n",
       "| intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation                                  |   55 |\n",
       "| intron_variant&amp;non_coding_transcript_variant&amp;feature_truncation                                  |   76 |\n",
       "| transcript_ablation                                                                              |   62 |\n",
       "| 5_prime_UTR_variant&amp;feature_elongation                                                           |    5 |\n",
       "| 3_prime_UTR_variant&amp;feature_elongation                                                           |    4 |\n",
       "| coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        |   12 |\n",
       "| 5_prime_UTR_variant&amp;feature_truncation                                                           |    2 |\n",
       "| transcript_amplification                                                                         |    5 |\n",
       "| coding_sequence_variant&amp;feature_elongation                                                       |    7 |\n",
       "| coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                   |    1 |\n",
       "| coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    |    3 |\n",
       "| frameshift_variant&amp;feature_truncation                                                            |    5 |\n",
       "| inframe_deletion&amp;feature_truncation                                                              |    5 |\n",
       "| non_coding_transcript_exon_variant&amp;feature_truncation                                            |    8 |\n",
       "| intron_variant                                                                                   |    1 |\n",
       "| stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation     |    2 |\n",
       "| 3_prime_UTR_variant&amp;feature_truncation                                                           |    5 |\n",
       "| coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                        |    2 |\n",
       "| non_coding_transcript_exon_variant&amp;feature_elongation                                            |    4 |\n",
       "| stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation          |    3 |\n",
       "| start_lost&amp;start_retained_variant&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation |    1 |\n",
       "| non_coding_transcript_exon_variant&amp;intron_variant&amp;feature_elongation                             |    1 |\n",
       "| 3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                                            |    1 |\n",
       "| stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                         |    1 |\n",
       "| non_coding_transcript_exon_variant&amp;intron_variant&amp;feature_truncation                             |    1 |\n",
       "\n"
      ],
      "text/plain": [
       "   Consequence                                                                                     \n",
       "1  intergenic_variant                                                                              \n",
       "2  upstream_gene_variant                                                                           \n",
       "3  downstream_gene_variant                                                                         \n",
       "4  intron_variant&feature_truncation                                                               \n",
       "5  intron_variant&feature_elongation                                                               \n",
       "6  coding_sequence_variant&5_prime_UTR_variant&intron_variant                                      \n",
       "7  intron_variant&non_coding_transcript_variant&feature_elongation                                 \n",
       "8  intron_variant&non_coding_transcript_variant&feature_truncation                                 \n",
       "9  transcript_ablation                                                                             \n",
       "10 5_prime_UTR_variant&feature_elongation                                                          \n",
       "11 3_prime_UTR_variant&feature_elongation                                                          \n",
       "12 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "13 5_prime_UTR_variant&feature_truncation                                                          \n",
       "14 transcript_amplification                                                                        \n",
       "15 coding_sequence_variant&feature_elongation                                                      \n",
       "16 coding_sequence_variant&5_prime_UTR_variant&feature_truncation                                  \n",
       "17 coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation                   \n",
       "18 frameshift_variant&feature_truncation                                                           \n",
       "19 inframe_deletion&feature_truncation                                                             \n",
       "20 non_coding_transcript_exon_variant&feature_truncation                                           \n",
       "21 intron_variant                                                                                  \n",
       "22 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation    \n",
       "23 3_prime_UTR_variant&feature_truncation                                                          \n",
       "24 coding_sequence_variant&intron_variant&feature_elongation                                       \n",
       "25 non_coding_transcript_exon_variant&feature_elongation                                           \n",
       "26 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation         \n",
       "27 start_lost&start_retained_variant&coding_sequence_variant&5_prime_UTR_variant&feature_truncation\n",
       "28 non_coding_transcript_exon_variant&intron_variant&feature_elongation                            \n",
       "29 3_prime_UTR_variant&intron_variant&feature_truncation                                           \n",
       "30 stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                        \n",
       "31 non_coding_transcript_exon_variant&intron_variant&feature_truncation                            \n",
       "   N   \n",
       "1  7983\n",
       "2   492\n",
       "3   505\n",
       "4  2182\n",
       "5  1613\n",
       "6     5\n",
       "7    55\n",
       "8    76\n",
       "9    62\n",
       "10    5\n",
       "11    4\n",
       "12   12\n",
       "13    2\n",
       "14    5\n",
       "15    7\n",
       "16    1\n",
       "17    3\n",
       "18    5\n",
       "19    5\n",
       "20    8\n",
       "21    1\n",
       "22    2\n",
       "23    5\n",
       "24    2\n",
       "25    4\n",
       "26    3\n",
       "27    1\n",
       "28    1\n",
       "29    1\n",
       "30    1\n",
       "31    1"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#summarize the SV by the functional annotation\n",
    "\n",
    "auto_angus[, .(.N), by = .(Consequence)]\n",
    "auto_UCD[, .(.N), by = .(Consequence)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 62 × 4</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>Consequence</th><th scope=col>IMPACT</th><th scope=col>SYMBOL</th><th scope=col>Gene</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000033360</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000049984</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000048551</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U6  </td><td>ENSBTAG00000052454</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000024003</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000040367</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000049320</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>CD24</td><td>ENSBTAG00000039046</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000052602</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000054178</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>RGS2</td><td>ENSBTAG00000020620</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000054814</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000049055</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000032114</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000054175</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000051208</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000054580</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000052986</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000050847</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000048627</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U6  </td><td>ENSBTAG00000043473</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U1  </td><td>ENSBTAG00000028923</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000048409</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000046079</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000053784</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000052619</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U6  </td><td>ENSBTAG00000051742</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000049950</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>    </td><td>ENSBTAG00000052479</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U3  </td><td>ENSBTAG00000036858</td></tr>\n",
       "\t<tr><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000052165</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000053316</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U3     </td><td>ENSBTAG00000049977</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000049772</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000052305</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000053258</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>5S_rRNA</td><td>ENSBTAG00000044438</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U6     </td><td>ENSBTAG00000052540</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000050094</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000049312</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000050466</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000053472</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000052005</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000045713</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000045729</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000015811</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000027787</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000034433</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>SNORA70</td><td>ENSBTAG00000044530</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000050735</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000042490</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U2     </td><td>ENSBTAG00000053819</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000054689</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000045403</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000049649</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000045111</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000050912</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U3     </td><td>ENSBTAG00000050100</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>       </td><td>ENSBTAG00000049723</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>SNORD22</td><td>ENSBTAG00000053112</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 62 × 4\n",
       "\\begin{tabular}{r|llll}\n",
       " Consequence & IMPACT & SYMBOL & Gene\\\\\n",
       " <chr> & <chr> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000033360\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000049984\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000048551\\\\\n",
       "\t transcript\\_ablation & HIGH & U6   & ENSBTAG00000052454\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000024003\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000040367\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000049320\\\\\n",
       "\t transcript\\_ablation & HIGH & CD24 & ENSBTAG00000039046\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000052602\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000054178\\\\\n",
       "\t transcript\\_ablation & HIGH & RGS2 & ENSBTAG00000020620\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000054814\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000049055\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000032114\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000054175\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000051208\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000054580\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000052986\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000050847\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000048627\\\\\n",
       "\t transcript\\_ablation & HIGH & U6   & ENSBTAG00000043473\\\\\n",
       "\t transcript\\_ablation & HIGH & U1   & ENSBTAG00000028923\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000048409\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000046079\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000053784\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000052619\\\\\n",
       "\t transcript\\_ablation & HIGH & U6   & ENSBTAG00000051742\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000049950\\\\\n",
       "\t transcript\\_ablation & HIGH &      & ENSBTAG00000052479\\\\\n",
       "\t transcript\\_ablation & HIGH & U3   & ENSBTAG00000036858\\\\\n",
       "\t ⋮ & ⋮ & ⋮ & ⋮\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000052165\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000053316\\\\\n",
       "\t transcript\\_ablation & HIGH & U3      & ENSBTAG00000049977\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000049772\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000052305\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000053258\\\\\n",
       "\t transcript\\_ablation & HIGH & 5S\\_rRNA & ENSBTAG00000044438\\\\\n",
       "\t transcript\\_ablation & HIGH & U6      & ENSBTAG00000052540\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000050094\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000049312\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000050466\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000053472\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000052005\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000045713\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000045729\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000015811\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000027787\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000034433\\\\\n",
       "\t transcript\\_ablation & HIGH & SNORA70 & ENSBTAG00000044530\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000050735\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000042490\\\\\n",
       "\t transcript\\_ablation & HIGH & U2      & ENSBTAG00000053819\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000054689\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000045403\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000049649\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000045111\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000050912\\\\\n",
       "\t transcript\\_ablation & HIGH & U3      & ENSBTAG00000050100\\\\\n",
       "\t transcript\\_ablation & HIGH &         & ENSBTAG00000049723\\\\\n",
       "\t transcript\\_ablation & HIGH & SNORD22 & ENSBTAG00000053112\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 62 × 4\n",
       "\n",
       "| Consequence &lt;chr&gt; | IMPACT &lt;chr&gt; | SYMBOL &lt;chr&gt; | Gene &lt;chr&gt; |\n",
       "|---|---|---|---|\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000033360 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000049984 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000048551 |\n",
       "| transcript_ablation | HIGH | U6   | ENSBTAG00000052454 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000024003 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000040367 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000049320 |\n",
       "| transcript_ablation | HIGH | CD24 | ENSBTAG00000039046 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000052602 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000054178 |\n",
       "| transcript_ablation | HIGH | RGS2 | ENSBTAG00000020620 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000054814 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000049055 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000032114 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000054175 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000051208 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000054580 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000052986 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000050847 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000048627 |\n",
       "| transcript_ablation | HIGH | U6   | ENSBTAG00000043473 |\n",
       "| transcript_ablation | HIGH | U1   | ENSBTAG00000028923 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000048409 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000046079 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000053784 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000052619 |\n",
       "| transcript_ablation | HIGH | U6   | ENSBTAG00000051742 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000049950 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000052479 |\n",
       "| transcript_ablation | HIGH | U3   | ENSBTAG00000036858 |\n",
       "| ⋮ | ⋮ | ⋮ | ⋮ |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000052165 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000053316 |\n",
       "| transcript_ablation | HIGH | U3      | ENSBTAG00000049977 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000049772 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000052305 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000053258 |\n",
       "| transcript_ablation | HIGH | 5S_rRNA | ENSBTAG00000044438 |\n",
       "| transcript_ablation | HIGH | U6      | ENSBTAG00000052540 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000050094 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000049312 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000050466 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000053472 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000052005 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000045713 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000045729 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000015811 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000027787 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000034433 |\n",
       "| transcript_ablation | HIGH | SNORA70 | ENSBTAG00000044530 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000050735 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000042490 |\n",
       "| transcript_ablation | HIGH | U2      | ENSBTAG00000053819 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000054689 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000045403 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000049649 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000045111 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000050912 |\n",
       "| transcript_ablation | HIGH | U3      | ENSBTAG00000050100 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBTAG00000049723 |\n",
       "| transcript_ablation | HIGH | SNORD22 | ENSBTAG00000053112 |\n",
       "\n"
      ],
      "text/plain": [
       "   Consequence         IMPACT SYMBOL  Gene              \n",
       "1  transcript_ablation HIGH           ENSBTAG00000033360\n",
       "2  transcript_ablation HIGH           ENSBTAG00000049984\n",
       "3  transcript_ablation HIGH           ENSBTAG00000048551\n",
       "4  transcript_ablation HIGH   U6      ENSBTAG00000052454\n",
       "5  transcript_ablation HIGH           ENSBTAG00000024003\n",
       "6  transcript_ablation HIGH           ENSBTAG00000040367\n",
       "7  transcript_ablation HIGH           ENSBTAG00000049320\n",
       "8  transcript_ablation HIGH   CD24    ENSBTAG00000039046\n",
       "9  transcript_ablation HIGH           ENSBTAG00000052602\n",
       "10 transcript_ablation HIGH           ENSBTAG00000054178\n",
       "11 transcript_ablation HIGH   RGS2    ENSBTAG00000020620\n",
       "12 transcript_ablation HIGH           ENSBTAG00000054814\n",
       "13 transcript_ablation HIGH           ENSBTAG00000049055\n",
       "14 transcript_ablation HIGH           ENSBTAG00000032114\n",
       "15 transcript_ablation HIGH           ENSBTAG00000054175\n",
       "16 transcript_ablation HIGH           ENSBTAG00000051208\n",
       "17 transcript_ablation HIGH           ENSBTAG00000054580\n",
       "18 transcript_ablation HIGH           ENSBTAG00000052986\n",
       "19 transcript_ablation HIGH           ENSBTAG00000050847\n",
       "20 transcript_ablation HIGH           ENSBTAG00000048627\n",
       "21 transcript_ablation HIGH   U6      ENSBTAG00000043473\n",
       "22 transcript_ablation HIGH   U1      ENSBTAG00000028923\n",
       "23 transcript_ablation HIGH           ENSBTAG00000048409\n",
       "24 transcript_ablation HIGH           ENSBTAG00000046079\n",
       "25 transcript_ablation HIGH           ENSBTAG00000053784\n",
       "26 transcript_ablation HIGH           ENSBTAG00000052619\n",
       "27 transcript_ablation HIGH   U6      ENSBTAG00000051742\n",
       "28 transcript_ablation HIGH           ENSBTAG00000049950\n",
       "29 transcript_ablation HIGH           ENSBTAG00000052479\n",
       "30 transcript_ablation HIGH   U3      ENSBTAG00000036858\n",
       "⋮  ⋮                   ⋮      ⋮       ⋮                 \n",
       "33 transcript_ablation HIGH           ENSBTAG00000052165\n",
       "34 transcript_ablation HIGH           ENSBTAG00000053316\n",
       "35 transcript_ablation HIGH   U3      ENSBTAG00000049977\n",
       "36 transcript_ablation HIGH           ENSBTAG00000049772\n",
       "37 transcript_ablation HIGH           ENSBTAG00000052305\n",
       "38 transcript_ablation HIGH           ENSBTAG00000053258\n",
       "39 transcript_ablation HIGH   5S_rRNA ENSBTAG00000044438\n",
       "40 transcript_ablation HIGH   U6      ENSBTAG00000052540\n",
       "41 transcript_ablation HIGH           ENSBTAG00000050094\n",
       "42 transcript_ablation HIGH           ENSBTAG00000049312\n",
       "43 transcript_ablation HIGH           ENSBTAG00000050466\n",
       "44 transcript_ablation HIGH           ENSBTAG00000053472\n",
       "45 transcript_ablation HIGH           ENSBTAG00000052005\n",
       "46 transcript_ablation HIGH           ENSBTAG00000045713\n",
       "47 transcript_ablation HIGH           ENSBTAG00000045729\n",
       "48 transcript_ablation HIGH           ENSBTAG00000015811\n",
       "49 transcript_ablation HIGH           ENSBTAG00000027787\n",
       "50 transcript_ablation HIGH           ENSBTAG00000034433\n",
       "51 transcript_ablation HIGH   SNORA70 ENSBTAG00000044530\n",
       "52 transcript_ablation HIGH           ENSBTAG00000050735\n",
       "53 transcript_ablation HIGH           ENSBTAG00000042490\n",
       "54 transcript_ablation HIGH   U2      ENSBTAG00000053819\n",
       "55 transcript_ablation HIGH           ENSBTAG00000054689\n",
       "56 transcript_ablation HIGH           ENSBTAG00000045403\n",
       "57 transcript_ablation HIGH           ENSBTAG00000049649\n",
       "58 transcript_ablation HIGH           ENSBTAG00000045111\n",
       "59 transcript_ablation HIGH           ENSBTAG00000050912\n",
       "60 transcript_ablation HIGH   U3      ENSBTAG00000050100\n",
       "61 transcript_ablation HIGH           ENSBTAG00000049723\n",
       "62 transcript_ablation HIGH   SNORD22 ENSBTAG00000053112"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "auto_UCD[Consequence %like%'transcript_ablation',c('Consequence','IMPACT','SYMBOL','Gene')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 51 × 4</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>Consequence</th><th scope=col>IMPACT</th><th scope=col>SYMBOL</th><th scope=col>Gene</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000027107</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U6             </td><td>ENSBIXG00000025339</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000025070</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000004663</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000023414</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000004900</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000027304</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000028262</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000005650</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000020663</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000018497</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000025035</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000003908</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000026517</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>CUL4B          </td><td>ENSBIXG00000005654</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000024937</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000006030</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U6             </td><td>ENSBIXG00000020274</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000000062</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000023459</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000023343</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000002403</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000019433</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000017488</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000016853</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000002473</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000016065</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000020689</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U1             </td><td>ENSBIXG00000009041</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000004221</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000021091</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000019682</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000003067</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000017671</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000019889</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000018477</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U6             </td><td>ENSBIXG00000016210</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>Telomerase-vert</td><td>ENSBIXG00000015339</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>SNORA74        </td><td>ENSBIXG00000014153</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000015546</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000001739</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000014890</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000013697</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000005992</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>U6             </td><td>ENSBIXG00000011774</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000009379</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000008284</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000008221</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000013127</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>SNORD22        </td><td>ENSBIXG00000028701</td></tr>\n",
       "\t<tr><td>transcript_ablation</td><td>HIGH</td><td>               </td><td>ENSBIXG00000029094</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 51 × 4\n",
       "\\begin{tabular}{r|llll}\n",
       " Consequence & IMPACT & SYMBOL & Gene\\\\\n",
       " <chr> & <chr> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000027107\\\\\n",
       "\t transcript\\_ablation & HIGH & U6              & ENSBIXG00000025339\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000025070\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000004663\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000023414\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000004900\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000027304\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000028262\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000005650\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000020663\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000018497\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000025035\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000003908\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000026517\\\\\n",
       "\t transcript\\_ablation & HIGH & CUL4B           & ENSBIXG00000005654\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000024937\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000006030\\\\\n",
       "\t transcript\\_ablation & HIGH & U6              & ENSBIXG00000020274\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000000062\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000023459\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000023343\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000002403\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000019433\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000017488\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000016853\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000002473\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000016065\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000020689\\\\\n",
       "\t transcript\\_ablation & HIGH & U1              & ENSBIXG00000009041\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000004221\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000021091\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000019682\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000003067\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000017671\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000019889\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000018477\\\\\n",
       "\t transcript\\_ablation & HIGH & U6              & ENSBIXG00000016210\\\\\n",
       "\t transcript\\_ablation & HIGH & Telomerase-vert & ENSBIXG00000015339\\\\\n",
       "\t transcript\\_ablation & HIGH & SNORA74         & ENSBIXG00000014153\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000015546\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000001739\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000014890\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000013697\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000005992\\\\\n",
       "\t transcript\\_ablation & HIGH & U6              & ENSBIXG00000011774\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000009379\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000008284\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000008221\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000013127\\\\\n",
       "\t transcript\\_ablation & HIGH & SNORD22         & ENSBIXG00000028701\\\\\n",
       "\t transcript\\_ablation & HIGH &                 & ENSBIXG00000029094\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 51 × 4\n",
       "\n",
       "| Consequence &lt;chr&gt; | IMPACT &lt;chr&gt; | SYMBOL &lt;chr&gt; | Gene &lt;chr&gt; |\n",
       "|---|---|---|---|\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000027107 |\n",
       "| transcript_ablation | HIGH | U6              | ENSBIXG00000025339 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000025070 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000004663 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000023414 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000004900 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000027304 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000028262 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000005650 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000020663 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000018497 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000025035 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000003908 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000026517 |\n",
       "| transcript_ablation | HIGH | CUL4B           | ENSBIXG00000005654 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000024937 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000006030 |\n",
       "| transcript_ablation | HIGH | U6              | ENSBIXG00000020274 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000000062 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000023459 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000023343 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000002403 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000019433 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000017488 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000016853 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000002473 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000016065 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000020689 |\n",
       "| transcript_ablation | HIGH | U1              | ENSBIXG00000009041 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000004221 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000021091 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000019682 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000003067 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000017671 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000019889 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000018477 |\n",
       "| transcript_ablation | HIGH | U6              | ENSBIXG00000016210 |\n",
       "| transcript_ablation | HIGH | Telomerase-vert | ENSBIXG00000015339 |\n",
       "| transcript_ablation | HIGH | SNORA74         | ENSBIXG00000014153 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000015546 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000001739 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000014890 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000013697 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000005992 |\n",
       "| transcript_ablation | HIGH | U6              | ENSBIXG00000011774 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000009379 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000008284 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000008221 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000013127 |\n",
       "| transcript_ablation | HIGH | SNORD22         | ENSBIXG00000028701 |\n",
       "| transcript_ablation | HIGH | <!----> | ENSBIXG00000029094 |\n",
       "\n"
      ],
      "text/plain": [
       "   Consequence         IMPACT SYMBOL          Gene              \n",
       "1  transcript_ablation HIGH                   ENSBIXG00000027107\n",
       "2  transcript_ablation HIGH   U6              ENSBIXG00000025339\n",
       "3  transcript_ablation HIGH                   ENSBIXG00000025070\n",
       "4  transcript_ablation HIGH                   ENSBIXG00000004663\n",
       "5  transcript_ablation HIGH                   ENSBIXG00000023414\n",
       "6  transcript_ablation HIGH                   ENSBIXG00000004900\n",
       "7  transcript_ablation HIGH                   ENSBIXG00000027304\n",
       "8  transcript_ablation HIGH                   ENSBIXG00000028262\n",
       "9  transcript_ablation HIGH                   ENSBIXG00000005650\n",
       "10 transcript_ablation HIGH                   ENSBIXG00000020663\n",
       "11 transcript_ablation HIGH                   ENSBIXG00000018497\n",
       "12 transcript_ablation HIGH                   ENSBIXG00000025035\n",
       "13 transcript_ablation HIGH                   ENSBIXG00000003908\n",
       "14 transcript_ablation HIGH                   ENSBIXG00000026517\n",
       "15 transcript_ablation HIGH   CUL4B           ENSBIXG00000005654\n",
       "16 transcript_ablation HIGH                   ENSBIXG00000024937\n",
       "17 transcript_ablation HIGH                   ENSBIXG00000006030\n",
       "18 transcript_ablation HIGH   U6              ENSBIXG00000020274\n",
       "19 transcript_ablation HIGH                   ENSBIXG00000000062\n",
       "20 transcript_ablation HIGH                   ENSBIXG00000023459\n",
       "21 transcript_ablation HIGH                   ENSBIXG00000023343\n",
       "22 transcript_ablation HIGH                   ENSBIXG00000002403\n",
       "23 transcript_ablation HIGH                   ENSBIXG00000019433\n",
       "24 transcript_ablation HIGH                   ENSBIXG00000017488\n",
       "25 transcript_ablation HIGH                   ENSBIXG00000016853\n",
       "26 transcript_ablation HIGH                   ENSBIXG00000002473\n",
       "27 transcript_ablation HIGH                   ENSBIXG00000016065\n",
       "28 transcript_ablation HIGH                   ENSBIXG00000020689\n",
       "29 transcript_ablation HIGH   U1              ENSBIXG00000009041\n",
       "30 transcript_ablation HIGH                   ENSBIXG00000004221\n",
       "31 transcript_ablation HIGH                   ENSBIXG00000021091\n",
       "32 transcript_ablation HIGH                   ENSBIXG00000019682\n",
       "33 transcript_ablation HIGH                   ENSBIXG00000003067\n",
       "34 transcript_ablation HIGH                   ENSBIXG00000017671\n",
       "35 transcript_ablation HIGH                   ENSBIXG00000019889\n",
       "36 transcript_ablation HIGH                   ENSBIXG00000018477\n",
       "37 transcript_ablation HIGH   U6              ENSBIXG00000016210\n",
       "38 transcript_ablation HIGH   Telomerase-vert ENSBIXG00000015339\n",
       "39 transcript_ablation HIGH   SNORA74         ENSBIXG00000014153\n",
       "40 transcript_ablation HIGH                   ENSBIXG00000015546\n",
       "41 transcript_ablation HIGH                   ENSBIXG00000001739\n",
       "42 transcript_ablation HIGH                   ENSBIXG00000014890\n",
       "43 transcript_ablation HIGH                   ENSBIXG00000013697\n",
       "44 transcript_ablation HIGH                   ENSBIXG00000005992\n",
       "45 transcript_ablation HIGH   U6              ENSBIXG00000011774\n",
       "46 transcript_ablation HIGH                   ENSBIXG00000009379\n",
       "47 transcript_ablation HIGH                   ENSBIXG00000008284\n",
       "48 transcript_ablation HIGH                   ENSBIXG00000008221\n",
       "49 transcript_ablation HIGH                   ENSBIXG00000013127\n",
       "50 transcript_ablation HIGH   SNORD22         ENSBIXG00000028701\n",
       "51 transcript_ablation HIGH                   ENSBIXG00000029094"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "auto_angus[Consequence %like%'transcript_ablation',c('Consequence','IMPACT','SYMBOL','Gene')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'U6'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'CD24'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'RGS2'</li>\n",
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       "\t<li>''</li>\n",
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       "\t<li>''</li>\n",
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       "\t<li>'U3'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'5S_rRNA'</li>\n",
       "\t<li>'U6'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
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       "\t<li>'SNORA70'</li>\n",
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       "\t<li>''</li>\n",
       "\t<li>'U2'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'U3'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'SNORD22'</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item ''\n",
       "\\item ''\n",
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       "\\item 'U6'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'CD24'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'RGS2'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'U6'\n",
       "\\item 'U1'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'U6'\n",
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       "\\item ''\n",
       "\\item 'U3'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'U3'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item '5S\\_rRNA'\n",
       "\\item 'U6'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'SNORA70'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'U2'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'U3'\n",
       "\\item ''\n",
       "\\item 'SNORD22'\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. ''\n",
       "2. ''\n",
       "3. ''\n",
       "4. 'U6'\n",
       "5. ''\n",
       "6. ''\n",
       "7. ''\n",
       "8. 'CD24'\n",
       "9. ''\n",
       "10. ''\n",
       "11. 'RGS2'\n",
       "12. ''\n",
       "13. ''\n",
       "14. ''\n",
       "15. ''\n",
       "16. ''\n",
       "17. ''\n",
       "18. ''\n",
       "19. ''\n",
       "20. ''\n",
       "21. 'U6'\n",
       "22. 'U1'\n",
       "23. ''\n",
       "24. ''\n",
       "25. ''\n",
       "26. ''\n",
       "27. 'U6'\n",
       "28. ''\n",
       "29. ''\n",
       "30. 'U3'\n",
       "31. ''\n",
       "32. ''\n",
       "33. ''\n",
       "34. ''\n",
       "35. 'U3'\n",
       "36. ''\n",
       "37. ''\n",
       "38. ''\n",
       "39. '5S_rRNA'\n",
       "40. 'U6'\n",
       "41. ''\n",
       "42. ''\n",
       "43. ''\n",
       "44. ''\n",
       "45. ''\n",
       "46. ''\n",
       "47. ''\n",
       "48. ''\n",
       "49. ''\n",
       "50. ''\n",
       "51. 'SNORA70'\n",
       "52. ''\n",
       "53. ''\n",
       "54. 'U2'\n",
       "55. ''\n",
       "56. ''\n",
       "57. ''\n",
       "58. ''\n",
       "59. ''\n",
       "60. 'U3'\n",
       "61. ''\n",
       "62. 'SNORD22'\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1] \"\"        \"\"        \"\"        \"U6\"      \"\"        \"\"        \"\"       \n",
       " [8] \"CD24\"    \"\"        \"\"        \"RGS2\"    \"\"        \"\"        \"\"       \n",
       "[15] \"\"        \"\"        \"\"        \"\"        \"\"        \"\"        \"U6\"     \n",
       "[22] \"U1\"      \"\"        \"\"        \"\"        \"\"        \"U6\"      \"\"       \n",
       "[29] \"\"        \"U3\"      \"\"        \"\"        \"\"        \"\"        \"U3\"     \n",
       "[36] \"\"        \"\"        \"\"        \"5S_rRNA\" \"U6\"      \"\"        \"\"       \n",
       "[43] \"\"        \"\"        \"\"        \"\"        \"\"        \"\"        \"\"       \n",
       "[50] \"\"        \"SNORA70\" \"\"        \"\"        \"U2\"      \"\"        \"\"       \n",
       "[57] \"\"        \"\"        \"\"        \"U3\"      \"\"        \"SNORD22\""
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<ol class=list-inline>\n",
       "\t<li>''</li>\n",
       "\t<li>'U6'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'CUL4B'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'U6'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'U1'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'U6'</li>\n",
       "\t<li>'Telomerase-vert'</li>\n",
       "\t<li>'SNORA74'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'U6'</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>''</li>\n",
       "\t<li>'SNORD22'</li>\n",
       "\t<li>''</li>\n",
       "</ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item ''\n",
       "\\item 'U6'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'CUL4B'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'U6'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'U1'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'U6'\n",
       "\\item 'Telomerase-vert'\n",
       "\\item 'SNORA74'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'U6'\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item ''\n",
       "\\item 'SNORD22'\n",
       "\\item ''\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. ''\n",
       "2. 'U6'\n",
       "3. ''\n",
       "4. ''\n",
       "5. ''\n",
       "6. ''\n",
       "7. ''\n",
       "8. ''\n",
       "9. ''\n",
       "10. ''\n",
       "11. ''\n",
       "12. ''\n",
       "13. ''\n",
       "14. ''\n",
       "15. 'CUL4B'\n",
       "16. ''\n",
       "17. ''\n",
       "18. 'U6'\n",
       "19. ''\n",
       "20. ''\n",
       "21. ''\n",
       "22. ''\n",
       "23. ''\n",
       "24. ''\n",
       "25. ''\n",
       "26. ''\n",
       "27. ''\n",
       "28. ''\n",
       "29. 'U1'\n",
       "30. ''\n",
       "31. ''\n",
       "32. ''\n",
       "33. ''\n",
       "34. ''\n",
       "35. ''\n",
       "36. ''\n",
       "37. 'U6'\n",
       "38. 'Telomerase-vert'\n",
       "39. 'SNORA74'\n",
       "40. ''\n",
       "41. ''\n",
       "42. ''\n",
       "43. ''\n",
       "44. ''\n",
       "45. 'U6'\n",
       "46. ''\n",
       "47. ''\n",
       "48. ''\n",
       "49. ''\n",
       "50. 'SNORD22'\n",
       "51. ''\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       " [1] \"\"                \"U6\"              \"\"                \"\"               \n",
       " [5] \"\"                \"\"                \"\"                \"\"               \n",
       " [9] \"\"                \"\"                \"\"                \"\"               \n",
       "[13] \"\"                \"\"                \"CUL4B\"           \"\"               \n",
       "[17] \"\"                \"U6\"              \"\"                \"\"               \n",
       "[21] \"\"                \"\"                \"\"                \"\"               \n",
       "[25] \"\"                \"\"                \"\"                \"\"               \n",
       "[29] \"U1\"              \"\"                \"\"                \"\"               \n",
       "[33] \"\"                \"\"                \"\"                \"\"               \n",
       "[37] \"U6\"              \"Telomerase-vert\" \"SNORA74\"         \"\"               \n",
       "[41] \"\"                \"\"                \"\"                \"\"               \n",
       "[45] \"U6\"              \"\"                \"\"                \"\"               \n",
       "[49] \"\"                \"SNORD22\"         \"\"               "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "auto_UCD[Consequence %like%'transcript_ablation',SYMBOL]\n",
    "auto_angus[Consequence%like%'transcript_ablation',SYMBOL]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "DEL_Angus=auto_angus[SVTYPE=='DEL',c('CHROM','POS','SYMBOL','Consequence','IMPACT','SVLEN','Gene',\"Feature_type\",\"Feature\",\"BIOTYPE\",'EXON','INTRON')]\n",
    "INS_Angus=auto_angus[SVTYPE=='INS',c('CHROM','POS','SYMBOL','Consequence','IMPACT','SVLEN','Gene',\"Feature_type\",\"Feature\",\"BIOTYPE\",'EXON','INTRON')]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "DEL_UCD=auto_UCD[SVTYPE=='DEL',c('CHROM','POS','SYMBOL','Consequence','IMPACT','SVLEN','Gene',\"Feature_type\",\"Feature\",\"BIOTYPE\",'EXON','INTRON')]\n",
    "INS_UCD=auto_UCD[SVTYPE=='INS',c('CHROM','POS','SYMBOL','Consequence','IMPACT','SVLEN','Gene',\"Feature_type\",\"Feature\",\"BIOTYPE\",'EXON','INTRON')]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "`summarise()` ungrouping output (override with `.groups` argument)\n",
      "`summarise()` ungrouping output (override with `.groups` argument)\n",
      "`summarise()` ungrouping output (override with `.groups` argument)\n",
      "`summarise()` ungrouping output (override with `.groups` argument)\n"
     ]
    }
   ],
   "source": [
    "#plot sv length\n",
    "#classify sv by length\n",
    "#SV < 1kb\n",
    "x=bind_rows(UCD %>% filter(SVTYPE==\"INS\") %>% filter(SVLEN<1000) %>% mutate(bin=ceiling(abs(SVLEN)/100)*100) %>% group_by(bin) %>% summarize(count=n()),\n",
    "            UCD %>% filter(SVTYPE==\"DEL\") %>% filter(SVLEN>-1000) %>% mutate(bin=ceiling(abs(SVLEN)/100)*100) %>% group_by(bin) %>% summarize(count=n()) %>% mutate(bin=-1*bin))\n",
    "#SV > lkb\n",
    "y = bind_rows(UCD %>% filter(SVTYPE==\"INS\") %>% filter(SVLEN>=1000) %>% mutate(bin=round(abs(SVLEN)/1000)*1000) %>% group_by(bin) %>% summarize(count=n()),\n",
    "              UCD %>% filter(SVTYPE==\"DEL\") %>% filter(SVLEN<= -1000) %>% mutate(bin=round(abs(SVLEN)/1000)*1000) %>% group_by(bin) %>% summarize(count=n()) %>% mutate(bin=-1*bin))\n",
    "\n",
    "#group SV > 10kb into one category\n",
    "#f=with(y,sum(y[bin < -10000, 2]))\n",
    "#y$bin[y$bin <= -11000 ] <- -11000\n",
    "#c=rbind(y %>% filter(bin> -11000),c(-11000,f))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 23 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SYMBOL</th><th scope=col>Consequence</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>ARHGEF10L</td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                   </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                                      </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                   </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>PCLO     </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                                      </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                                      </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                                      </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation               </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                                      </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                                      </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation               </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                   </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                                      </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                                      </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 23 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " SYMBOL & Consequence\\\\\n",
       " <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t ARHGEF10L & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                                   \\\\\n",
       "\t           & frameshift\\_variant\\&feature\\_truncation                                                                      \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                                   \\\\\n",
       "\t PCLO      & frameshift\\_variant\\&feature\\_truncation                                                                      \\\\\n",
       "\t           & frameshift\\_variant\\&feature\\_truncation                                                                      \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    \\\\\n",
       "\t           & frameshift\\_variant\\&feature\\_truncation                                                                      \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation               \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation\\\\\n",
       "\t           & frameshift\\_variant\\&feature\\_truncation                                                                      \\\\\n",
       "\t           & frameshift\\_variant\\&feature\\_truncation                                                                      \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation               \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                                   \\\\\n",
       "\t           & frameshift\\_variant\\&feature\\_truncation                                                                      \\\\\n",
       "\t           & frameshift\\_variant\\&feature\\_truncation                                                                      \\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 23 × 2\n",
       "\n",
       "| SYMBOL &lt;chr&gt; | Consequence &lt;chr&gt; |\n",
       "|---|---|\n",
       "| ARHGEF10L | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                    |\n",
       "| <!----> | frameshift_variant&amp;feature_truncation                                                                       |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                    |\n",
       "| PCLO      | frameshift_variant&amp;feature_truncation                                                                       |\n",
       "| <!----> | frameshift_variant&amp;feature_truncation                                                                       |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     |\n",
       "| <!----> | frameshift_variant&amp;feature_truncation                                                                       |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation                |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation |\n",
       "| <!----> | frameshift_variant&amp;feature_truncation                                                                       |\n",
       "| <!----> | frameshift_variant&amp;feature_truncation                                                                       |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation                |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                    |\n",
       "| <!----> | frameshift_variant&amp;feature_truncation                                                                       |\n",
       "| <!----> | frameshift_variant&amp;feature_truncation                                                                       |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     |\n",
       "\n"
      ],
      "text/plain": [
       "   SYMBOL   \n",
       "1  ARHGEF10L\n",
       "2           \n",
       "3           \n",
       "4  PCLO     \n",
       "5           \n",
       "6           \n",
       "7           \n",
       "8           \n",
       "9           \n",
       "10          \n",
       "11          \n",
       "12          \n",
       "13          \n",
       "14          \n",
       "15          \n",
       "16          \n",
       "17          \n",
       "18          \n",
       "19          \n",
       "20          \n",
       "21          \n",
       "22          \n",
       "23          \n",
       "   Consequence                                                                                                \n",
       "1  stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                                   \n",
       "2  frameshift_variant&feature_truncation                                                                      \n",
       "3  stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                                   \n",
       "4  frameshift_variant&feature_truncation                                                                      \n",
       "5  frameshift_variant&feature_truncation                                                                      \n",
       "6  stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "7  frameshift_variant&feature_truncation                                                                      \n",
       "8  stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "9  stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "10 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "11 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant&feature_truncation\n",
       "12 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "13 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation               \n",
       "14 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant&feature_truncation\n",
       "15 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "16 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant&feature_truncation\n",
       "17 frameshift_variant&feature_truncation                                                                      \n",
       "18 frameshift_variant&feature_truncation                                                                      \n",
       "19 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation               \n",
       "20 stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                                   \n",
       "21 frameshift_variant&feature_truncation                                                                      \n",
       "22 frameshift_variant&feature_truncation                                                                      \n",
       "23 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 17 × 2</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SYMBOL</th><th scope=col>Consequence</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>PLA2G2A</td><td>transcript_amplification                                                                        </td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>CRNN   </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                           </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation    </span></td></tr>\n",
       "\t<tr><td>       </td><td>transcript_amplification                                                                        </td></tr>\n",
       "\t<tr><td>       </td><td>transcript_amplification                                                                        </td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation         </span></td></tr>\n",
       "\t<tr><td>       </td><td>transcript_amplification                                                                        </td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td>start_lost&amp;start_retained_variant&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation         </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation    </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                           </span></td></tr>\n",
       "\t<tr><td>       </td><td>transcript_amplification                                                                        </td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                           </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                        </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>MAST4  </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                           </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>RREB1  </span></td><td><span style=white-space:pre-wrap>frameshift_variant&amp;feature_truncation                                                           </span></td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation         </span></td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 17 × 2\n",
       "\\begin{tabular}{r|ll}\n",
       " SYMBOL & Consequence\\\\\n",
       " <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t PLA2G2A & transcript\\_amplification                                                                        \\\\\n",
       "\t CRNN    & frameshift\\_variant\\&feature\\_truncation                                                           \\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation    \\\\\n",
       "\t         & transcript\\_amplification                                                                        \\\\\n",
       "\t         & transcript\\_amplification                                                                        \\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation         \\\\\n",
       "\t         & transcript\\_amplification                                                                        \\\\\n",
       "\t         & start\\_lost\\&start\\_retained\\_variant\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&feature\\_truncation\\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation         \\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation    \\\\\n",
       "\t         & frameshift\\_variant\\&feature\\_truncation                                                           \\\\\n",
       "\t         & transcript\\_amplification                                                                        \\\\\n",
       "\t         & frameshift\\_variant\\&feature\\_truncation                                                           \\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                        \\\\\n",
       "\t MAST4   & frameshift\\_variant\\&feature\\_truncation                                                           \\\\\n",
       "\t RREB1   & frameshift\\_variant\\&feature\\_truncation                                                           \\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation         \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 17 × 2\n",
       "\n",
       "| SYMBOL &lt;chr&gt; | Consequence &lt;chr&gt; |\n",
       "|---|---|\n",
       "| PLA2G2A | transcript_amplification                                                                         |\n",
       "| CRNN    | frameshift_variant&amp;feature_truncation                                                            |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation     |\n",
       "| <!----> | transcript_amplification                                                                         |\n",
       "| <!----> | transcript_amplification                                                                         |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation          |\n",
       "| <!----> | transcript_amplification                                                                         |\n",
       "| <!----> | start_lost&amp;start_retained_variant&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation          |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation     |\n",
       "| <!----> | frameshift_variant&amp;feature_truncation                                                            |\n",
       "| <!----> | transcript_amplification                                                                         |\n",
       "| <!----> | frameshift_variant&amp;feature_truncation                                                            |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                         |\n",
       "| MAST4   | frameshift_variant&amp;feature_truncation                                                            |\n",
       "| RREB1   | frameshift_variant&amp;feature_truncation                                                            |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation          |\n",
       "\n"
      ],
      "text/plain": [
       "   SYMBOL \n",
       "1  PLA2G2A\n",
       "2  CRNN   \n",
       "3         \n",
       "4         \n",
       "5         \n",
       "6         \n",
       "7         \n",
       "8         \n",
       "9         \n",
       "10        \n",
       "11        \n",
       "12        \n",
       "13        \n",
       "14        \n",
       "15 MAST4  \n",
       "16 RREB1  \n",
       "17        \n",
       "   Consequence                                                                                     \n",
       "1  transcript_amplification                                                                        \n",
       "2  frameshift_variant&feature_truncation                                                           \n",
       "3  stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation    \n",
       "4  transcript_amplification                                                                        \n",
       "5  transcript_amplification                                                                        \n",
       "6  stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation         \n",
       "7  transcript_amplification                                                                        \n",
       "8  start_lost&start_retained_variant&coding_sequence_variant&5_prime_UTR_variant&feature_truncation\n",
       "9  stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation         \n",
       "10 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation    \n",
       "11 frameshift_variant&feature_truncation                                                           \n",
       "12 transcript_amplification                                                                        \n",
       "13 frameshift_variant&feature_truncation                                                           \n",
       "14 stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                        \n",
       "15 frameshift_variant&feature_truncation                                                           \n",
       "16 frameshift_variant&feature_truncation                                                           \n",
       "17 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation         "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "auto_angus[(IMPACT=='HIGH'&Consequence!='transcript_ablation'),c('SYMBOL','Consequence')]\n",
    "auto_UCD[(IMPACT=='HIGH'&Consequence!='transcript_ablation'),c('SYMBOL','Consequence')]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 13 × 5</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SYMBOL</th><th scope=col>Consequence</th><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ALT</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>         </td><td>intergenic_variant                                        </td><td>1 </td><td>65303659</td><td>N[3:95515321[ </td></tr>\n",
       "\t<tr><td>         </td><td>intergenic_variant                                        </td><td>2 </td><td>39579871</td><td>N[6:58499253[ </td></tr>\n",
       "\t<tr><td>         </td><td>intergenic_variant                                        </td><td>6 </td><td> 6845739</td><td>N[19:14420094[</td></tr>\n",
       "\t<tr><td>7SK      </td><td>intergenic_variant                                        </td><td>9 </td><td> 7438066</td><td>N[18:24221720[</td></tr>\n",
       "\t<tr><td>UBE2J1   </td><td>3_prime_UTR_variant                                       </td><td>9 </td><td>22468064</td><td>N[14:52592262[</td></tr>\n",
       "\t<tr><td>         </td><td>intergenic_variant                                        </td><td>9 </td><td>23945058</td><td>N[X:111253682[</td></tr>\n",
       "\t<tr><td>MAPK1IP1L</td><td>intergenic_variant                                        </td><td>10</td><td>51280023</td><td>N[14:68469736[</td></tr>\n",
       "\t<tr><td>MAPK1IP1L</td><td>intergenic_variant                                        </td><td>10</td><td>60715020</td><td>N[11:83590718[</td></tr>\n",
       "\t<tr><td>         </td><td>intergenic_variant                                        </td><td>11</td><td>52327961</td><td>N[21:61533002[</td></tr>\n",
       "\t<tr><td>         </td><td>intergenic_variant                                        </td><td>17</td><td>26540604</td><td>N[X:113473415[</td></tr>\n",
       "\t<tr><td>KRTDAP   </td><td>intergenic_variant                                        </td><td>18</td><td>10866335</td><td>N[25:28119758[</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>ADGRG5   </span></td><td>coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant</td><td>18</td><td>33328933</td><td>N[19:38711484[</td></tr>\n",
       "\t<tr><td>CPEB1    </td><td>intergenic_variant                                        </td><td>21</td><td> 2566081</td><td>N[28:26544857[</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 13 × 5\n",
       "\\begin{tabular}{r|lllll}\n",
       " SYMBOL & Consequence & CHROM & POS & ALT\\\\\n",
       " <chr> & <chr> & <chr> & <int> & <chr>\\\\\n",
       "\\hline\n",
       "\t           & intergenic\\_variant                                         & 1  & 65303659 & N{[}3:95515321{[} \\\\\n",
       "\t           & intergenic\\_variant                                         & 2  & 39579871 & N{[}6:58499253{[} \\\\\n",
       "\t           & intergenic\\_variant                                         & 6  &  6845739 & N{[}19:14420094{[}\\\\\n",
       "\t 7SK       & intergenic\\_variant                                         & 9  &  7438066 & N{[}18:24221720{[}\\\\\n",
       "\t UBE2J1    & 3\\_prime\\_UTR\\_variant                                        & 9  & 22468064 & N{[}14:52592262{[}\\\\\n",
       "\t           & intergenic\\_variant                                         & 9  & 23945058 & N{[}X:111253682{[}\\\\\n",
       "\t MAPK1IP1L & intergenic\\_variant                                         & 10 & 51280023 & N{[}14:68469736{[}\\\\\n",
       "\t MAPK1IP1L & intergenic\\_variant                                         & 10 & 60715020 & N{[}11:83590718{[}\\\\\n",
       "\t           & intergenic\\_variant                                         & 11 & 52327961 & N{[}21:61533002{[}\\\\\n",
       "\t           & intergenic\\_variant                                         & 17 & 26540604 & N{[}X:113473415{[}\\\\\n",
       "\t KRTDAP    & intergenic\\_variant                                         & 18 & 10866335 & N{[}25:28119758{[}\\\\\n",
       "\t ADGRG5    & coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant & 18 & 33328933 & N{[}19:38711484{[}\\\\\n",
       "\t CPEB1     & intergenic\\_variant                                         & 21 &  2566081 & N{[}28:26544857{[}\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 13 × 5\n",
       "\n",
       "| SYMBOL &lt;chr&gt; | Consequence &lt;chr&gt; | CHROM &lt;chr&gt; | POS &lt;int&gt; | ALT &lt;chr&gt; |\n",
       "|---|---|---|---|---|\n",
       "| <!----> | intergenic_variant                                         | 1  | 65303659 | N[3:95515321[  |\n",
       "| <!----> | intergenic_variant                                         | 2  | 39579871 | N[6:58499253[  |\n",
       "| <!----> | intergenic_variant                                         | 6  |  6845739 | N[19:14420094[ |\n",
       "| 7SK       | intergenic_variant                                         | 9  |  7438066 | N[18:24221720[ |\n",
       "| UBE2J1    | 3_prime_UTR_variant                                        | 9  | 22468064 | N[14:52592262[ |\n",
       "| <!----> | intergenic_variant                                         | 9  | 23945058 | N[X:111253682[ |\n",
       "| MAPK1IP1L | intergenic_variant                                         | 10 | 51280023 | N[14:68469736[ |\n",
       "| MAPK1IP1L | intergenic_variant                                         | 10 | 60715020 | N[11:83590718[ |\n",
       "| <!----> | intergenic_variant                                         | 11 | 52327961 | N[21:61533002[ |\n",
       "| <!----> | intergenic_variant                                         | 17 | 26540604 | N[X:113473415[ |\n",
       "| KRTDAP    | intergenic_variant                                         | 18 | 10866335 | N[25:28119758[ |\n",
       "| ADGRG5    | coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant | 18 | 33328933 | N[19:38711484[ |\n",
       "| CPEB1     | intergenic_variant                                         | 21 |  2566081 | N[28:26544857[ |\n",
       "\n"
      ],
      "text/plain": [
       "   SYMBOL    Consequence                                                CHROM\n",
       "1            intergenic_variant                                         1    \n",
       "2            intergenic_variant                                         2    \n",
       "3            intergenic_variant                                         6    \n",
       "4  7SK       intergenic_variant                                         9    \n",
       "5  UBE2J1    3_prime_UTR_variant                                        9    \n",
       "6            intergenic_variant                                         9    \n",
       "7  MAPK1IP1L intergenic_variant                                         10   \n",
       "8  MAPK1IP1L intergenic_variant                                         10   \n",
       "9            intergenic_variant                                         11   \n",
       "10           intergenic_variant                                         17   \n",
       "11 KRTDAP    intergenic_variant                                         18   \n",
       "12 ADGRG5    coding_sequence_variant&3_prime_UTR_variant&intron_variant 18   \n",
       "13 CPEB1     intergenic_variant                                         21   \n",
       "   POS      ALT           \n",
       "1  65303659 N[3:95515321[ \n",
       "2  39579871 N[6:58499253[ \n",
       "3   6845739 N[19:14420094[\n",
       "4   7438066 N[18:24221720[\n",
       "5  22468064 N[14:52592262[\n",
       "6  23945058 N[X:111253682[\n",
       "7  51280023 N[14:68469736[\n",
       "8  60715020 N[11:83590718[\n",
       "9  52327961 N[21:61533002[\n",
       "10 26540604 N[X:113473415[\n",
       "11 10866335 N[25:28119758[\n",
       "12 33328933 N[19:38711484[\n",
       "13  2566081 N[28:26544857["
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 22 × 5</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SYMBOL</th><th scope=col>Consequence</th><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ALT</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td><span style=white-space:pre-wrap>GRIK1   </span></td><td>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant</td><td>1 </td><td> 6043134</td><td>N[27:6219504[ </td></tr>\n",
       "\t<tr><td>THBS3   </td><td>intergenic_variant                                        </td><td>3 </td><td>14298807</td><td>N[10:25269073[</td></tr>\n",
       "\t<tr><td>TRMT10A </td><td>intergenic_variant                                        </td><td>6 </td><td> 5445333</td><td>N[8:34789102[ </td></tr>\n",
       "\t<tr><td>TRMT10A </td><td>intergenic_variant                                        </td><td>6 </td><td> 5445759</td><td>N[8:34785216[ </td></tr>\n",
       "\t<tr><td>        </td><td>intergenic_variant                                        </td><td>6 </td><td> 6408589</td><td>N[19:14466702[</td></tr>\n",
       "\t<tr><td>PNOC    </td><td>intergenic_variant                                        </td><td>8 </td><td>10211906</td><td>N[21:32952273[</td></tr>\n",
       "\t<tr><td>PDCD1LG2</td><td>intergenic_variant                                        </td><td>8 </td><td>34785147</td><td>N[11:43480451[</td></tr>\n",
       "\t<tr><td>PDCD1LG2</td><td>intergenic_variant                                        </td><td>8 </td><td>34789014</td><td>N[11:43480485[</td></tr>\n",
       "\t<tr><td>        </td><td>intergenic_variant                                        </td><td>8 </td><td>79447889</td><td>N[X:127909506[</td></tr>\n",
       "\t<tr><td>WDR54   </td><td>intergenic_variant                                        </td><td>11</td><td> 3462191</td><td>N[24:19061784[</td></tr>\n",
       "\t<tr><td>GPR75   </td><td>intergenic_variant                                        </td><td>11</td><td>26636122</td><td>N[16:48884294[</td></tr>\n",
       "\t<tr><td>VPS54   </td><td>intergenic_variant                                        </td><td>11</td><td>52659127</td><td>N[21:62485426[</td></tr>\n",
       "\t<tr><td>        </td><td>intergenic_variant                                        </td><td>11</td><td>56618676</td><td>N[13:59573550[</td></tr>\n",
       "\t<tr><td>OBI1    </td><td>intergenic_variant                                        </td><td>12</td><td>50331559</td><td>N[13:73918244[</td></tr>\n",
       "\t<tr><td>CRLS1   </td><td>intergenic_variant                                        </td><td>13</td><td>36708032</td><td>N[17:67873211[</td></tr>\n",
       "\t<tr><td>IL18    </td><td>intergenic_variant                                        </td><td>15</td><td>15841861</td><td>N[29:41056156[</td></tr>\n",
       "\t<tr><td>PYCR2   </td><td>intergenic_variant                                        </td><td>16</td><td>19583939</td><td>N[20:49537396[</td></tr>\n",
       "\t<tr><td>FGF18   </td><td>intergenic_variant                                        </td><td>20</td><td> 1853444</td><td>N[23:5631676[ </td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>GABRA5  </span></td><td>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant</td><td>21</td><td> 1620621</td><td>N[28:4289093[ </td></tr>\n",
       "\t<tr><td>VPS33B  </td><td>intergenic_variant                                        </td><td>21</td><td> 3178454</td><td>N[28:26766922[</td></tr>\n",
       "\t<tr><td>CCDC178 </td><td>intergenic_variant                                        </td><td>24</td><td>12956626</td><td>N[25:27903364[</td></tr>\n",
       "\t<tr><td>        </td><td>intergenic_variant                                        </td><td>24</td><td>36802471</td><td>N[X:59756458[ </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 22 × 5\n",
       "\\begin{tabular}{r|lllll}\n",
       " SYMBOL & Consequence & CHROM & POS & ALT\\\\\n",
       " <chr> & <chr> & <chr> & <int> & <chr>\\\\\n",
       "\\hline\n",
       "\t GRIK1    & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant & 1  &  6043134 & N{[}27:6219504{[} \\\\\n",
       "\t THBS3    & intergenic\\_variant                                         & 3  & 14298807 & N{[}10:25269073{[}\\\\\n",
       "\t TRMT10A  & intergenic\\_variant                                         & 6  &  5445333 & N{[}8:34789102{[} \\\\\n",
       "\t TRMT10A  & intergenic\\_variant                                         & 6  &  5445759 & N{[}8:34785216{[} \\\\\n",
       "\t          & intergenic\\_variant                                         & 6  &  6408589 & N{[}19:14466702{[}\\\\\n",
       "\t PNOC     & intergenic\\_variant                                         & 8  & 10211906 & N{[}21:32952273{[}\\\\\n",
       "\t PDCD1LG2 & intergenic\\_variant                                         & 8  & 34785147 & N{[}11:43480451{[}\\\\\n",
       "\t PDCD1LG2 & intergenic\\_variant                                         & 8  & 34789014 & N{[}11:43480485{[}\\\\\n",
       "\t          & intergenic\\_variant                                         & 8  & 79447889 & N{[}X:127909506{[}\\\\\n",
       "\t WDR54    & intergenic\\_variant                                         & 11 &  3462191 & N{[}24:19061784{[}\\\\\n",
       "\t GPR75    & intergenic\\_variant                                         & 11 & 26636122 & N{[}16:48884294{[}\\\\\n",
       "\t VPS54    & intergenic\\_variant                                         & 11 & 52659127 & N{[}21:62485426{[}\\\\\n",
       "\t          & intergenic\\_variant                                         & 11 & 56618676 & N{[}13:59573550{[}\\\\\n",
       "\t OBI1     & intergenic\\_variant                                         & 12 & 50331559 & N{[}13:73918244{[}\\\\\n",
       "\t CRLS1    & intergenic\\_variant                                         & 13 & 36708032 & N{[}17:67873211{[}\\\\\n",
       "\t IL18     & intergenic\\_variant                                         & 15 & 15841861 & N{[}29:41056156{[}\\\\\n",
       "\t PYCR2    & intergenic\\_variant                                         & 16 & 19583939 & N{[}20:49537396{[}\\\\\n",
       "\t FGF18    & intergenic\\_variant                                         & 20 &  1853444 & N{[}23:5631676{[} \\\\\n",
       "\t GABRA5   & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant & 21 &  1620621 & N{[}28:4289093{[} \\\\\n",
       "\t VPS33B   & intergenic\\_variant                                         & 21 &  3178454 & N{[}28:26766922{[}\\\\\n",
       "\t CCDC178  & intergenic\\_variant                                         & 24 & 12956626 & N{[}25:27903364{[}\\\\\n",
       "\t          & intergenic\\_variant                                         & 24 & 36802471 & N{[}X:59756458{[} \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 22 × 5\n",
       "\n",
       "| SYMBOL &lt;chr&gt; | Consequence &lt;chr&gt; | CHROM &lt;chr&gt; | POS &lt;int&gt; | ALT &lt;chr&gt; |\n",
       "|---|---|---|---|---|\n",
       "| GRIK1    | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant | 1  |  6043134 | N[27:6219504[  |\n",
       "| THBS3    | intergenic_variant                                         | 3  | 14298807 | N[10:25269073[ |\n",
       "| TRMT10A  | intergenic_variant                                         | 6  |  5445333 | N[8:34789102[  |\n",
       "| TRMT10A  | intergenic_variant                                         | 6  |  5445759 | N[8:34785216[  |\n",
       "| <!----> | intergenic_variant                                         | 6  |  6408589 | N[19:14466702[ |\n",
       "| PNOC     | intergenic_variant                                         | 8  | 10211906 | N[21:32952273[ |\n",
       "| PDCD1LG2 | intergenic_variant                                         | 8  | 34785147 | N[11:43480451[ |\n",
       "| PDCD1LG2 | intergenic_variant                                         | 8  | 34789014 | N[11:43480485[ |\n",
       "| <!----> | intergenic_variant                                         | 8  | 79447889 | N[X:127909506[ |\n",
       "| WDR54    | intergenic_variant                                         | 11 |  3462191 | N[24:19061784[ |\n",
       "| GPR75    | intergenic_variant                                         | 11 | 26636122 | N[16:48884294[ |\n",
       "| VPS54    | intergenic_variant                                         | 11 | 52659127 | N[21:62485426[ |\n",
       "| <!----> | intergenic_variant                                         | 11 | 56618676 | N[13:59573550[ |\n",
       "| OBI1     | intergenic_variant                                         | 12 | 50331559 | N[13:73918244[ |\n",
       "| CRLS1    | intergenic_variant                                         | 13 | 36708032 | N[17:67873211[ |\n",
       "| IL18     | intergenic_variant                                         | 15 | 15841861 | N[29:41056156[ |\n",
       "| PYCR2    | intergenic_variant                                         | 16 | 19583939 | N[20:49537396[ |\n",
       "| FGF18    | intergenic_variant                                         | 20 |  1853444 | N[23:5631676[  |\n",
       "| GABRA5   | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant | 21 |  1620621 | N[28:4289093[  |\n",
       "| VPS33B   | intergenic_variant                                         | 21 |  3178454 | N[28:26766922[ |\n",
       "| CCDC178  | intergenic_variant                                         | 24 | 12956626 | N[25:27903364[ |\n",
       "| <!----> | intergenic_variant                                         | 24 | 36802471 | N[X:59756458[  |\n",
       "\n"
      ],
      "text/plain": [
       "   SYMBOL   Consequence                                                CHROM\n",
       "1  GRIK1    coding_sequence_variant&5_prime_UTR_variant&intron_variant 1    \n",
       "2  THBS3    intergenic_variant                                         3    \n",
       "3  TRMT10A  intergenic_variant                                         6    \n",
       "4  TRMT10A  intergenic_variant                                         6    \n",
       "5           intergenic_variant                                         6    \n",
       "6  PNOC     intergenic_variant                                         8    \n",
       "7  PDCD1LG2 intergenic_variant                                         8    \n",
       "8  PDCD1LG2 intergenic_variant                                         8    \n",
       "9           intergenic_variant                                         8    \n",
       "10 WDR54    intergenic_variant                                         11   \n",
       "11 GPR75    intergenic_variant                                         11   \n",
       "12 VPS54    intergenic_variant                                         11   \n",
       "13          intergenic_variant                                         11   \n",
       "14 OBI1     intergenic_variant                                         12   \n",
       "15 CRLS1    intergenic_variant                                         13   \n",
       "16 IL18     intergenic_variant                                         15   \n",
       "17 PYCR2    intergenic_variant                                         16   \n",
       "18 FGF18    intergenic_variant                                         20   \n",
       "19 GABRA5   coding_sequence_variant&5_prime_UTR_variant&intron_variant 21   \n",
       "20 VPS33B   intergenic_variant                                         21   \n",
       "21 CCDC178  intergenic_variant                                         24   \n",
       "22          intergenic_variant                                         24   \n",
       "   POS      ALT           \n",
       "1   6043134 N[27:6219504[ \n",
       "2  14298807 N[10:25269073[\n",
       "3   5445333 N[8:34789102[ \n",
       "4   5445759 N[8:34785216[ \n",
       "5   6408589 N[19:14466702[\n",
       "6  10211906 N[21:32952273[\n",
       "7  34785147 N[11:43480451[\n",
       "8  34789014 N[11:43480485[\n",
       "9  79447889 N[X:127909506[\n",
       "10  3462191 N[24:19061784[\n",
       "11 26636122 N[16:48884294[\n",
       "12 52659127 N[21:62485426[\n",
       "13 56618676 N[13:59573550[\n",
       "14 50331559 N[13:73918244[\n",
       "15 36708032 N[17:67873211[\n",
       "16 15841861 N[29:41056156[\n",
       "17 19583939 N[20:49537396[\n",
       "18  1853444 N[23:5631676[ \n",
       "19  1620621 N[28:4289093[ \n",
       "20  3178454 N[28:26766922[\n",
       "21 12956626 N[25:27903364[\n",
       "22 36802471 N[X:59756458[ "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "auto_angus[SVTYPE=='TRA',c('SYMBOL','Consequence','CHROM','POS','ALT')]\n",
    "auto_UCD[SVTYPE=='TRA',c('SYMBOL','Consequence','CHROM','POS','ALT')]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 37 × 6</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SYMBOL</th><th scope=col>Consequence</th><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ALT</th><th scope=col>SVTYPE</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td><span style=white-space:pre-wrap>GRIK1  </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                      </span></td><td>1 </td><td><span style=white-space:pre-wrap>  6043134</span></td><td><span style=white-space:pre-wrap>N[27:6219504[                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              </span></td><td>TRA</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>1 </td><td>139122525</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td>ZBTB40 </td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>2 </td><td>130314877</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td>SLC66A1</td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                      </span></td><td>2 </td><td>133347668</td><td><span style=white-space:pre-wrap>TGGCCTGGAACCGGAAGCGAGCAAGCCATCCTGCCCTTCTCCTTCCTCGAGGCATCG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                      </span></td><td>2 </td><td>133390927</td><td><span style=white-space:pre-wrap>TAGCTGGACAGGAGGGGACGGTAGCACATGGGGTCAGGACCACAGGGTCACACAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                  </span></td><td>3 </td><td><span style=white-space:pre-wrap>  5412142</span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                   </span></td><td>3 </td><td> 18249191</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                   </span></td><td>4 </td><td>105611739</td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>WC1    </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                      </span></td><td>5 </td><td>102812698</td><td><span style=white-space:pre-wrap>&lt;INV&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>INV</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                      </span></td><td>7 </td><td> 13159555</td><td><span style=white-space:pre-wrap>TTTTTCCAGGAGTCAACTCTCTCTTGTCTAGGATTTCTGTAAATCCTTGGGAATGCTATTAATGATTGTTTTCTACATAATTCATTATATTTATTATCGCTTTATTATGATTTATAGGAATGTTAGGAGTTTTCTATCTTGTGTGTGACTTAGTAAAGTCAACAGAGATAATATCT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation    </span></td><td>7 </td><td> 13545535</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>TPC3   </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                       </span></td><td>11</td><td><span style=white-space:pre-wrap>  1651085</span></td><td><span style=white-space:pre-wrap>&lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>DUP</td></tr>\n",
       "\t<tr><td>BPIFB5 </td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>13</td><td> 62805339</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                      </span></td><td>14</td><td><span style=white-space:pre-wrap>  1764120</span></td><td><span style=white-space:pre-wrap>CTTCCCTTCTCCACCTCTGCCCTGGGGCCTTCTCTACCCTCTGCCTGGGGTGGGGCTCCTCTCCACCTTTCTGCCCTGGGGGCTCCTTCTCCACCTCTGCCCCGGGGGCTCTTCTCCACCCTCTGCCCTGGGG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation         </span></td><td>14</td><td> 22091728</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td>start_lost&amp;start_retained_variant&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation</td><td>15</td><td> 45917281</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation         </span></td><td>15</td><td> 49056581</td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation    </span></td><td>16</td><td> 40718165</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>AJAP1  </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                      </span></td><td>16</td><td> 48586118</td><td><span style=white-space:pre-wrap>&lt;INV&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>INV</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                       </span></td><td>18</td><td> 51426332</td><td><span style=white-space:pre-wrap>&lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>DUP</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>18</td><td> 57221082</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                      </span></td><td>18</td><td> 60291404</td><td><span style=white-space:pre-wrap>AACATTCATAAGGTCTCTCTCCAGTATGTATTCCTGCCAATGTACAGTAAGAGCTGACCTGTAACCAAAGGCTTTGCCACATTCAGT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                        </span></td><td>18</td><td> 61826605</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>18</td><td> 62420558</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>OSCAR  </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>18</td><td> 63289444</td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>18</td><td> 65116599</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td>GABRA5 </td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                      </span></td><td>21</td><td><span style=white-space:pre-wrap>  1620621</span></td><td><span style=white-space:pre-wrap>N[28:4289093[                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              </span></td><td>TRA</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                   </span></td><td>21</td><td> 37876244</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>BTNL2  </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                      </span></td><td>23</td><td> 25882749</td><td>AATTATGATTCTGAAACCAGGGTTATATTCTAAGTCCCAGTTCTTTTCTCTTTTCACCAACTATTAGAGGACTGGCCTCACTCACTTACCTAATCCAAGAGGATTTAACCTTACTCTGGTATCATATCTGACCTGGAACTTATCCTTTCTGTGAGCTGTCATATCCCAAGAAGCTCTCTAATATCCTGCCTGCTGATCACAATCTGATATCTGATAACAAAGACCTTTACAGAAAATCCAATGGAAAATGCAACTTAGCCTAGAGGAGAGGCATGAGGAACAATCAAGTATTTGATTTGTGTCTCTAGAGAAAGGGGTAACAATTATCCCAATGGGACAGGAAAACAAAAATACAGTTAAAATAAGGAAGAAAATATAGCTAAATGTAAGGAGGAAAATCTGATCACTAAGATATAAATCTTGAAAATCCCATAAAGTGTGTAATTTCTGCATCAAACTTTCTCAGAAAGTTAATTGAGAGTGTGGGAGTGAGGAAATTTTTCAGAAATACTAGTCGAGAGAAACATGTTACATGTCATGTATATGAGGAATGTCAATTTTAGTTTTAGAGTGCAAAGCACACAATTTAAAATTAATACTTACAAAATAAACAGAAGCAATATGTACAACACAAGCAATAAAATGCAATGGAAATAAAAAAAAATATTTTAAATCACAGTGAATTAAAACAGAGAAGCCACACATAGGAGAAGAAGGAGCATTGAAAAAAG</td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                      </span></td><td>25</td><td><span style=white-space:pre-wrap>  2508710</span></td><td><span style=white-space:pre-wrap>&lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>DUP</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>26</td><td><span style=white-space:pre-wrap>  8623968</span></td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </span></td><td>DEL</td></tr>\n",
       "\t<tr><td>PLEKHS1</td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>26</td><td> 34224348</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>26</td><td> 50492889</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>RGR    </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>28</td><td> 39221430</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation         </span></td><td>29</td><td><span style=white-space:pre-wrap>  4648133</span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>CAPN1  </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                       </span></td><td>29</td><td> 43406186</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                      </span></td><td>29</td><td> 50204839</td><td><span style=white-space:pre-wrap>GGTGAGTCGCTGTGGAGGAGGGTCAGTCACACTGGAAGTAGAATGGAGTCTCTGAAAGTGGTCGCTGTGGAGGAAAGTCCTATCACCTGGTGGGGGTGGATGTCACTCTCCGTGGTCACTGTGGAGGAGGGTCTGTCACTCGTGGGGTAGAGACCCTCCGTGGTTGCACTGTGGAGGACGGACCTGTCACACTGTGGTGGGGGTGGAGTCCTCTCAGTGGTCGCTGTGGAAGAGGGTCCAGTCACTCGTGGGGTGGAGACCCCTCTGTAGTCACTGTGGAGAAGGTCCTGTCACACTGGTGAAGTGGAGAGTCCTCTC                                                                                                                                                                                                                                                                                                                                                                                                                             </span></td><td>INS</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 37 × 6\n",
       "\\begin{tabular}{r|llllll}\n",
       " SYMBOL & Consequence & CHROM & POS & ALT & SVTYPE\\\\\n",
       " <chr> & <chr> & <chr> & <int> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t GRIK1   & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant                                       & 1  &   6043134 & N{[}27:6219504{[}                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               & TRA\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 1  & 139122525 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t ZBTB40  & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 2  & 130314877 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t SLC66A1 & coding\\_sequence\\_variant\\&feature\\_elongation                                                       & 2  & 133347668 & TGGCCTGGAACCGGAAGCGAGCAAGCCATCCTGCCCTTCTCCTTCCTCGAGGCATCG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   & INS\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&feature\\_elongation                                                       & 2  & 133390927 & TAGCTGGACAGGAGGGGACGGTAGCACATGGGGTCAGGACCACAGGGTCACACAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     & INS\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&feature\\_truncation                                   & 3  &   5412142 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    & 3  &  18249191 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    & 4  & 105611739 & <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & DEL\\\\\n",
       "\t WC1     & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant                                       & 5  & 102812698 & <INV>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & INV\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&feature\\_elongation                                                       & 7  &  13159555 & TTTTTCCAGGAGTCAACTCTCTCTTGTCTAGGATTTCTGTAAATCCTTGGGAATGCTATTAATGATTGTTTTCTACATAATTCATTATATTTATTATCGCTTTATTATGATTTATAGGAATGTTAGGAGTTTTCTATCTTGTGTGTGACTTAGTAAAGTCAACAGAGATAATATCT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            & INS\\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation     & 7  &  13545535 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t TPC3    & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_elongation                                        & 11 &   1651085 & <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & DUP\\\\\n",
       "\t BPIFB5  & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 13 &  62805339 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&feature\\_elongation                                                       & 14 &   1764120 & CTTCCCTTCTCCACCTCTGCCCTGGGGCCTTCTCTACCCTCTGCCTGGGGTGGGGCTCCTCTCCACCTTTCTGCCCTGGGGGCTCCTTCTCCACCTCTGCCCCGGGGGCTCTTCTCCACCCTCTGCCCTGGGG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & INS\\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation          & 14 &  22091728 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & start\\_lost\\&start\\_retained\\_variant\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&feature\\_truncation & 15 &  45917281 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation          & 15 &  49056581 & <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & DEL\\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation     & 16 &  40718165 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t AJAP1   & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant                                       & 16 &  48586118 & <INV>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & INV\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_elongation                                        & 18 &  51426332 & <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & DUP\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 18 &  57221082 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&feature\\_elongation                                                       & 18 &  60291404 & AACATTCATAAGGTCTCTCTCCAGTATGTATTCCTGCCAATGTACAGTAAGAGCTGACCTGTAACCAAAGGCTTTGCCACATTCAGT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     & INS\\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                         & 18 &  61826605 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 18 &  62420558 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t OSCAR   & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 18 &  63289444 & <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & DEL\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 18 &  65116599 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t GABRA5  & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant                                       & 21 &   1620621 & N{[}28:4289093{[}                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               & TRA\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                    & 21 &  37876244 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t BTNL2   & coding\\_sequence\\_variant\\&feature\\_elongation                                                       & 23 &  25882749 & AATTATGATTCTGAAACCAGGGTTATATTCTAAGTCCCAGTTCTTTTCTCTTTTCACCAACTATTAGAGGACTGGCCTCACTCACTTACCTAATCCAAGAGGATTTAACCTTACTCTGGTATCATATCTGACCTGGAACTTATCCTTTCTGTGAGCTGTCATATCCCAAGAAGCTCTCTAATATCCTGCCTGCTGATCACAATCTGATATCTGATAACAAAGACCTTTACAGAAAATCCAATGGAAAATGCAACTTAGCCTAGAGGAGAGGCATGAGGAACAATCAAGTATTTGATTTGTGTCTCTAGAGAAAGGGGTAACAATTATCCCAATGGGACAGGAAAACAAAAATACAGTTAAAATAAGGAAGAAAATATAGCTAAATGTAAGGAGGAAAATCTGATCACTAAGATATAAATCTTGAAAATCCCATAAAGTGTGTAATTTCTGCATCAAACTTTCTCAGAAAGTTAATTGAGAGTGTGGGAGTGAGGAAATTTTTCAGAAATACTAGTCGAGAGAAACATGTTACATGTCATGTATATGAGGAATGTCAATTTTAGTTTTAGAGTGCAAAGCACACAATTTAAAATTAATACTTACAAAATAAACAGAAGCAATATGTACAACACAAGCAATAAAATGCAATGGAAATAAAAAAAAATATTTTAAATCACAGTGAATTAAAACAGAGAAGCCACACATAGGAGAAGAAGGAGCATTGAAAAAAG & INS\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant                                       & 25 &   2508710 & <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & DUP\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 26 &   8623968 & <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & DEL\\\\\n",
       "\t PLEKHS1 & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 26 &  34224348 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 26 &  50492889 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t RGR     & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 28 &  39221430 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation          & 29 &   4648133 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t CAPN1   & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                        & 29 &  43406186 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & DEL\\\\\n",
       "\t         & coding\\_sequence\\_variant\\&feature\\_elongation                                                       & 29 &  50204839 & GGTGAGTCGCTGTGGAGGAGGGTCAGTCACACTGGAAGTAGAATGGAGTCTCTGAAAGTGGTCGCTGTGGAGGAAAGTCCTATCACCTGGTGGGGGTGGATGTCACTCTCCGTGGTCACTGTGGAGGAGGGTCTGTCACTCGTGGGGTAGAGACCCTCCGTGGTTGCACTGTGGAGGACGGACCTGTCACACTGTGGTGGGGGTGGAGTCCTCTCAGTGGTCGCTGTGGAAGAGGGTCCAGTCACTCGTGGGGTGGAGACCCCTCTGTAGTCACTGTGGAGAAGGTCCTGTCACACTGGTGAAGTGGAGAGTCCTCTC                                                                                                                                                                                                                                                                                                                                                                                                                              & INS\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 37 × 6\n",
       "\n",
       "| SYMBOL &lt;chr&gt; | Consequence &lt;chr&gt; | CHROM &lt;chr&gt; | POS &lt;int&gt; | ALT &lt;chr&gt; | SVTYPE &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|\n",
       "| GRIK1   | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                       | 1  |   6043134 | N[27:6219504[                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | TRA |\n",
       "| <!----> | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 1  | 139122525 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| ZBTB40  | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 2  | 130314877 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| SLC66A1 | coding_sequence_variant&amp;feature_elongation                                                       | 2  | 133347668 | TGGCCTGGAACCGGAAGCGAGCAAGCCATCCTGCCCTTCTCCTTCCTCGAGGCATCG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | INS |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                       | 2  | 133390927 | TAGCTGGACAGGAGGGGACGGTAGCACATGGGGTCAGGACCACAGGGTCACACAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | INS |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                   | 3  |   5412142 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    | 3  |  18249191 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    | 4  | 105611739 | &lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | DEL |\n",
       "| WC1     | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                       | 5  | 102812698 | &lt;INV&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | INV |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                       | 7  |  13159555 | TTTTTCCAGGAGTCAACTCTCTCTTGTCTAGGATTTCTGTAAATCCTTGGGAATGCTATTAATGATTGTTTTCTACATAATTCATTATATTTATTATCGCTTTATTATGATTTATAGGAATGTTAGGAGTTTTCTATCTTGTGTGTGACTTAGTAAAGTCAACAGAGATAATATCT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | INS |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation     | 7  |  13545535 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| TPC3    | coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                        | 11 |   1651085 | &lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | DUP |\n",
       "| BPIFB5  | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 13 |  62805339 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                       | 14 |   1764120 | CTTCCCTTCTCCACCTCTGCCCTGGGGCCTTCTCTACCCTCTGCCTGGGGTGGGGCTCCTCTCCACCTTTCTGCCCTGGGGGCTCCTTCTCCACCTCTGCCCCGGGGGCTCTTCTCCACCCTCTGCCCTGGGG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | INS |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation          | 14 |  22091728 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | start_lost&amp;start_retained_variant&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation | 15 |  45917281 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation          | 15 |  49056581 | &lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | DEL |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation     | 16 |  40718165 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| AJAP1   | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                       | 16 |  48586118 | &lt;INV&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | INV |\n",
       "| <!----> | coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                        | 18 |  51426332 | &lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | DUP |\n",
       "| <!----> | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 18 |  57221082 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                       | 18 |  60291404 | AACATTCATAAGGTCTCTCTCCAGTATGTATTCCTGCCAATGTACAGTAAGAGCTGACCTGTAACCAAAGGCTTTGCCACATTCAGT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | INS |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                         | 18 |  61826605 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 18 |  62420558 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| OSCAR   | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 18 |  63289444 | &lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 18 |  65116599 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| GABRA5  | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                       | 21 |   1620621 | N[28:4289093[                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | TRA |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    | 21 |  37876244 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| BTNL2   | coding_sequence_variant&amp;feature_elongation                                                       | 23 |  25882749 | AATTATGATTCTGAAACCAGGGTTATATTCTAAGTCCCAGTTCTTTTCTCTTTTCACCAACTATTAGAGGACTGGCCTCACTCACTTACCTAATCCAAGAGGATTTAACCTTACTCTGGTATCATATCTGACCTGGAACTTATCCTTTCTGTGAGCTGTCATATCCCAAGAAGCTCTCTAATATCCTGCCTGCTGATCACAATCTGATATCTGATAACAAAGACCTTTACAGAAAATCCAATGGAAAATGCAACTTAGCCTAGAGGAGAGGCATGAGGAACAATCAAGTATTTGATTTGTGTCTCTAGAGAAAGGGGTAACAATTATCCCAATGGGACAGGAAAACAAAAATACAGTTAAAATAAGGAAGAAAATATAGCTAAATGTAAGGAGGAAAATCTGATCACTAAGATATAAATCTTGAAAATCCCATAAAGTGTGTAATTTCTGCATCAAACTTTCTCAGAAAGTTAATTGAGAGTGTGGGAGTGAGGAAATTTTTCAGAAATACTAGTCGAGAGAAACATGTTACATGTCATGTATATGAGGAATGTCAATTTTAGTTTTAGAGTGCAAAGCACACAATTTAAAATTAATACTTACAAAATAAACAGAAGCAATATGTACAACACAAGCAATAAAATGCAATGGAAATAAAAAAAAATATTTTAAATCACAGTGAATTAAAACAGAGAAGCCACACATAGGAGAAGAAGGAGCATTGAAAAAAG | INS |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                       | 25 |   2508710 | &lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | DUP |\n",
       "| <!----> | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 26 |   8623968 | &lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | DEL |\n",
       "| PLEKHS1 | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 26 |  34224348 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 26 |  50492889 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| RGR     | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 28 |  39221430 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation          | 29 |   4648133 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| CAPN1   | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                        | 29 |  43406186 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                       | 29 |  50204839 | GGTGAGTCGCTGTGGAGGAGGGTCAGTCACACTGGAAGTAGAATGGAGTCTCTGAAAGTGGTCGCTGTGGAGGAAAGTCCTATCACCTGGTGGGGGTGGATGTCACTCTCCGTGGTCACTGTGGAGGAGGGTCTGTCACTCGTGGGGTAGAGACCCTCCGTGGTTGCACTGTGGAGGACGGACCTGTCACACTGTGGTGGGGGTGGAGTCCTCTCAGTGGTCGCTGTGGAAGAGGGTCCAGTCACTCGTGGGGTGGAGACCCCTCTGTAGTCACTGTGGAGAAGGTCCTGTCACACTGGTGAAGTGGAGAGTCCTCTC                                                                                                                                                                                                                                                                                                                                                                                                                              | INS |\n",
       "\n"
      ],
      "text/plain": [
       "   SYMBOL \n",
       "1  GRIK1  \n",
       "2         \n",
       "3  ZBTB40 \n",
       "4  SLC66A1\n",
       "5         \n",
       "6         \n",
       "7         \n",
       "8         \n",
       "9  WC1    \n",
       "10        \n",
       "11        \n",
       "12 TPC3   \n",
       "13 BPIFB5 \n",
       "14        \n",
       "15        \n",
       "16        \n",
       "17        \n",
       "18        \n",
       "19 AJAP1  \n",
       "20        \n",
       "21        \n",
       "22        \n",
       "23        \n",
       "24        \n",
       "25 OSCAR  \n",
       "26        \n",
       "27 GABRA5 \n",
       "28        \n",
       "29 BTNL2  \n",
       "30        \n",
       "31        \n",
       "32 PLEKHS1\n",
       "33        \n",
       "34 RGR    \n",
       "35        \n",
       "36 CAPN1  \n",
       "37        \n",
       "   Consequence                                                                                     \n",
       "1  coding_sequence_variant&5_prime_UTR_variant&intron_variant                                      \n",
       "2  coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "3  coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "4  coding_sequence_variant&feature_elongation                                                      \n",
       "5  coding_sequence_variant&feature_elongation                                                      \n",
       "6  coding_sequence_variant&5_prime_UTR_variant&feature_truncation                                  \n",
       "7  coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation                   \n",
       "8  coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation                   \n",
       "9  coding_sequence_variant&5_prime_UTR_variant&intron_variant                                      \n",
       "10 coding_sequence_variant&feature_elongation                                                      \n",
       "11 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation    \n",
       "12 coding_sequence_variant&intron_variant&feature_elongation                                       \n",
       "13 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "14 coding_sequence_variant&feature_elongation                                                      \n",
       "15 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation         \n",
       "16 start_lost&start_retained_variant&coding_sequence_variant&5_prime_UTR_variant&feature_truncation\n",
       "17 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation         \n",
       "18 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation    \n",
       "19 coding_sequence_variant&5_prime_UTR_variant&intron_variant                                      \n",
       "20 coding_sequence_variant&intron_variant&feature_elongation                                       \n",
       "21 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "22 coding_sequence_variant&feature_elongation                                                      \n",
       "23 stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                        \n",
       "24 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "25 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "26 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "27 coding_sequence_variant&5_prime_UTR_variant&intron_variant                                      \n",
       "28 coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation                   \n",
       "29 coding_sequence_variant&feature_elongation                                                      \n",
       "30 coding_sequence_variant&5_prime_UTR_variant&intron_variant                                      \n",
       "31 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "32 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "33 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "34 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "35 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation         \n",
       "36 coding_sequence_variant&intron_variant&feature_truncation                                       \n",
       "37 coding_sequence_variant&feature_elongation                                                      \n",
       "   CHROM POS      \n",
       "1  1       6043134\n",
       "2  1     139122525\n",
       "3  2     130314877\n",
       "4  2     133347668\n",
       "5  2     133390927\n",
       "6  3       5412142\n",
       "7  3      18249191\n",
       "8  4     105611739\n",
       "9  5     102812698\n",
       "10 7      13159555\n",
       "11 7      13545535\n",
       "12 11      1651085\n",
       "13 13     62805339\n",
       "14 14      1764120\n",
       "15 14     22091728\n",
       "16 15     45917281\n",
       "17 15     49056581\n",
       "18 16     40718165\n",
       "19 16     48586118\n",
       "20 18     51426332\n",
       "21 18     57221082\n",
       "22 18     60291404\n",
       "23 18     61826605\n",
       "24 18     62420558\n",
       "25 18     63289444\n",
       "26 18     65116599\n",
       "27 21      1620621\n",
       "28 21     37876244\n",
       "29 23     25882749\n",
       "30 25      2508710\n",
       "31 26      8623968\n",
       "32 26     34224348\n",
       "33 26     50492889\n",
       "34 28     39221430\n",
       "35 29      4648133\n",
       "36 29     43406186\n",
       "37 29     50204839\n",
       "   ALT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        \n",
       "1  N[27:6219504[                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              \n",
       "2  N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "3  N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "4  TGGCCTGGAACCGGAAGCGAGCAAGCCATCCTGCCCTTCTCCTTCCTCGAGGCATCG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  \n",
       "5  TAGCTGGACAGGAGGGGACGGTAGCACATGGGGTCAGGACCACAGGGTCACACAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    \n",
       "6  N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "7  N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "8  <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "9  <INV>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "10 TTTTTCCAGGAGTCAACTCTCTCTTGTCTAGGATTTCTGTAAATCCTTGGGAATGCTATTAATGATTGTTTTCTACATAATTCATTATATTTATTATCGCTTTATTATGATTTATAGGAATGTTAGGAGTTTTCTATCTTGTGTGTGACTTAGTAAAGTCAACAGAGATAATATCT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           \n",
       "11 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "12 <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "13 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "14 CTTCCCTTCTCCACCTCTGCCCTGGGGCCTTCTCTACCCTCTGCCTGGGGTGGGGCTCCTCTCCACCTTTCTGCCCTGGGGGCTCCTTCTCCACCTCTGCCCCGGGGGCTCTTCTCCACCCTCTGCCCTGGGG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "15 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "16 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "17 <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "18 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "19 <INV>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "20 <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "21 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "22 AACATTCATAAGGTCTCTCTCCAGTATGTATTCCTGCCAATGTACAGTAAGAGCTGACCTGTAACCAAAGGCTTTGCCACATTCAGT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    \n",
       "23 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "24 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "25 <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "26 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "27 N[28:4289093[                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              \n",
       "28 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "29 AATTATGATTCTGAAACCAGGGTTATATTCTAAGTCCCAGTTCTTTTCTCTTTTCACCAACTATTAGAGGACTGGCCTCACTCACTTACCTAATCCAAGAGGATTTAACCTTACTCTGGTATCATATCTGACCTGGAACTTATCCTTTCTGTGAGCTGTCATATCCCAAGAAGCTCTCTAATATCCTGCCTGCTGATCACAATCTGATATCTGATAACAAAGACCTTTACAGAAAATCCAATGGAAAATGCAACTTAGCCTAGAGGAGAGGCATGAGGAACAATCAAGTATTTGATTTGTGTCTCTAGAGAAAGGGGTAACAATTATCCCAATGGGACAGGAAAACAAAAATACAGTTAAAATAAGGAAGAAAATATAGCTAAATGTAAGGAGGAAAATCTGATCACTAAGATATAAATCTTGAAAATCCCATAAAGTGTGTAATTTCTGCATCAAACTTTCTCAGAAAGTTAATTGAGAGTGTGGGAGTGAGGAAATTTTTCAGAAATACTAGTCGAGAGAAACATGTTACATGTCATGTATATGAGGAATGTCAATTTTAGTTTTAGAGTGCAAAGCACACAATTTAAAATTAATACTTACAAAATAAACAGAAGCAATATGTACAACACAAGCAATAAAATGCAATGGAAATAAAAAAAAATATTTTAAATCACAGTGAATTAAAACAGAGAAGCCACACATAGGAGAAGAAGGAGCATTGAAAAAAG\n",
       "30 <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "31 <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "32 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "33 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "34 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "35 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "36 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "37 GGTGAGTCGCTGTGGAGGAGGGTCAGTCACACTGGAAGTAGAATGGAGTCTCTGAAAGTGGTCGCTGTGGAGGAAAGTCCTATCACCTGGTGGGGGTGGATGTCACTCTCCGTGGTCACTGTGGAGGAGGGTCTGTCACTCGTGGGGTAGAGACCCTCCGTGGTTGCACTGTGGAGGACGGACCTGTCACACTGTGGTGGGGGTGGAGTCCTCTCAGTGGTCGCTGTGGAAGAGGGTCCAGTCACTCGTGGGGTGGAGACCCCTCTGTAGTCACTGTGGAGAAGGTCCTGTCACACTGGTGAAGTGGAGAGTCCTCTC                                                                                                                                                                                                                                                                                                                                                                                                                             \n",
       "   SVTYPE\n",
       "1  TRA   \n",
       "2  DEL   \n",
       "3  DEL   \n",
       "4  INS   \n",
       "5  INS   \n",
       "6  DEL   \n",
       "7  DEL   \n",
       "8  DEL   \n",
       "9  INV   \n",
       "10 INS   \n",
       "11 DEL   \n",
       "12 DUP   \n",
       "13 DEL   \n",
       "14 INS   \n",
       "15 DEL   \n",
       "16 DEL   \n",
       "17 DEL   \n",
       "18 DEL   \n",
       "19 INV   \n",
       "20 DUP   \n",
       "21 DEL   \n",
       "22 INS   \n",
       "23 DEL   \n",
       "24 DEL   \n",
       "25 DEL   \n",
       "26 DEL   \n",
       "27 TRA   \n",
       "28 DEL   \n",
       "29 INS   \n",
       "30 DUP   \n",
       "31 DEL   \n",
       "32 DEL   \n",
       "33 DEL   \n",
       "34 DEL   \n",
       "35 DEL   \n",
       "36 DEL   \n",
       "37 INS   "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 45 × 6</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SYMBOL</th><th scope=col>Consequence</th><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ALT</th><th scope=col>SVTYPE</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td>ARHGEF10L</td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                   </span></td><td>2 </td><td><span style=white-space:pre-wrap>  1406176</span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                             </span></td><td>2 </td><td>109966395</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                              </span></td><td>3 </td><td> 10637333</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                   </span></td><td>4 </td><td><span style=white-space:pre-wrap>  6744135</span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>C7orf57  </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td>4 </td><td>112138554</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                                 </span></td><td>5 </td><td> 27592200</td><td><span style=white-space:pre-wrap>&lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DUP</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td><td>5 </td><td> 58290107</td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant                                                 </span></td><td>5 </td><td>101700700</td><td><span style=white-space:pre-wrap>&lt;INV&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>INV</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                              </span></td><td>5 </td><td>102381998</td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>LMF2     </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                                 </span></td><td>5 </td><td>119154005</td><td><span style=white-space:pre-wrap>CCCCCCGCCGGCACGCCCGCCCCTCCGCGCCGGCCCCGCCCCGCCTCCGCGCCGGCCCCGCCCCG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td><td>6 </td><td>114481338</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                                 </span></td><td>7 </td><td> 41927433</td><td><span style=white-space:pre-wrap>TGACAACTACCACCACTACTCCAAGAACAAGCACTACAAGAAGGACAACCACCACCACTAAAACCCCAAAGGACAACTACTACCACTACTCCAAGAAACAGCCACTACAAGAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>C5orf15  </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td>7 </td><td> 65052970</td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                                  </span></td><td>7 </td><td>101977018</td><td><span style=white-space:pre-wrap>&lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DUP</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td><td>7 </td><td>107999583</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>ACER2    </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td>8 </td><td> 24574719</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                              </span></td><td>9 </td><td> 15493182</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td><td>9 </td><td> 92049306</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                                 </span></td><td>10</td><td> 27366642</td><td><span style=white-space:pre-wrap>&lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DUP</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>LYG1     </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td>11</td><td><span style=white-space:pre-wrap>  4319201</span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation</td><td>11</td><td> 13759801</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                                 </span></td><td>12</td><td> 73351320</td><td><span style=white-space:pre-wrap>CGTTCTTTTTTTTTTTTTCTTTTTTTTTTCTTTCTTTTTTACTTTTATTTTATTTTTAAACTTTACATAATTGTATTAGTTTTGCCAAACATCAAAGTGAATCCACCACAGAGTATACATGTGTTCCCCATCCTGAACCCTCCTCCCTCCTCCCTCCCCATACCATCCCTCTGGAGTCGTCCCAATGCACTAGCTACAAGCATCCAGTATGAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td><td>13</td><td> 20646968</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant                             </span></td><td>13</td><td> 20906813</td><td><span style=white-space:pre-wrap>&lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DUP</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation               </span></td><td>13</td><td> 25258768</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation</td><td>13</td><td> 77550072</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>DCHS1    </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant                             </span></td><td>15</td><td> 46356965</td><td><span style=white-space:pre-wrap>&lt;INV&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>INV</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td><td>15</td><td> 49323433</td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>USH2A    </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td>16</td><td> 18381410</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>WSCD2    </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                                 </span></td><td>17</td><td> 64326523</td><td><span style=white-space:pre-wrap>TGTTGGGGGCCAGAGTGAGGTACTCCGCCCATGGCAAGGTCATGAGGAAGGAGGCTCGGCTATCGCAAGTGAGGATCAGGCCTCAGGAGTCCCTAAATCCTCGGCGTCTACCCATAACCAGAGCCTGCCTACTTTACTACTTTGTGCTCTTACCTACACCTCCTGACTTTACGGGGCTGTCCCCACCCTCTTCGGAGAAGGAGTTAACCTAGAGCTCAGTCAATAAAAACTCTTGGGTGTGGCAAGAGTGTTTTAACCACTACAAACTCCTCTGAAGGTTCTCTGGCCCTGCCCTGACAGGCTCGTCCGGCCACATGTGAGTTGCTCGCAGCCTCCCAACCATGAGCTGAGATGCTTTGACCTTCACAAAAACAGGTTCCTTAGAAAAGTTAGAAAACTATTAGTATAAGTATAATGGGCCTAATTAGAAATTGTGTTGGTGAAGGGGTTTTTCATTTGCTGAGCCAATGTTTGTTGCTAAGTCTCATATCCTGCCACTTACACGTGTGAATATATAGAATTGACCTTTGATATTAATCACGTTAGACCTTAGGCTAAACCAAATTCTTTCCTTAACTAAAACCCACTACACCTCACCTGTAGGAGTGTAACTTTACTTAGGTGGCGTCTGTTTTGAGAATAATCAGCCCTGGAGAAATAAGTGTGTCCTGATTGACTGACCGCTGTCACAAAGGGAGAGGAGTAAATAAATTGTCAGCAGGCCCCCTGGCCCAGAGATGATGTAACACCCCTAAGACCTCTGTATACATTTTGTGTGAAGCACCTGACTTTAATAAAGTCAGGACTGCTGTCCCCACGTGACTTTTGTATAACATCTTAGTGTATAAAAACAGACTCTGGAAAATAAAAAATTTGGGGATCAGTTTCTCAAAATACTGGTCTCCCCATGTCTCTCTCTCCCTCGGCTGAGTCTCCATCTGGAGGCGCAGGAACCCGCAAGCTTACTAATTTTGCCTGGGCTTCTAGATCCGACCGGGAGGCCTCAGTGTCTCCTCTCCTTCGGGAGAGCGGAAGGACGATACAAACCTACGTAAGTGATGCAAGCTTCTTGTCTTGAAGTTTTGTGGTCCCAACGTAAACCAAGCTACTCGGCCTCTTTTCTCCACTGAATTTTCCTACTGAGCTATCGCACTTATTCTAGTACTCTTTATATCTCTAATTAATATCTATTGAAACTATACGTATCTGACCCTCGCCCGATGCCGTCTCTCGCCAGTACCCTGGATCGGCAGGGCTGGTCCTGGGTT                                                    </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                                 </span></td><td>17</td><td> 71655478</td><td><span style=white-space:pre-wrap>TCCTTCCTCCTCCGCCGCCCTCCGCCCCACCTCCTCCCCCTGCCGCCCCCTCCCGCCCCACCTCCTCGCCGCCCCTCCGCCCCT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                              </span></td><td>18</td><td><span style=white-space:pre-wrap>   699541</span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation</td><td>18</td><td><span style=white-space:pre-wrap>  4687966</span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;3_prime_UTR_variant                                                                </span></td><td>18</td><td> 18071065</td><td><span style=white-space:pre-wrap>&lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DUP</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>ADGRG5   </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant                                                 </span></td><td>18</td><td> 33328933</td><td><span style=white-space:pre-wrap>N[19:38711484[                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </span></td><td>TRA</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>STX8     </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                             </span></td><td>19</td><td> 28840835</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation               </span></td><td>20</td><td> 25550031</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                                 </span></td><td>22</td><td> 16418735</td><td>AATTCTGAAGCCGGTATCTCCAAGAACGGGCAGACCCGTGAGCATGCTCCTTCTGTCTTACACCCTGGGTGTGAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCACCCTATAGCCAGAAGAGATACGAAGAAATTGTTAAGGAAGCCAGCACCTACATTAAGAAATTGGCTACAACCCCCACACGGTAGCATTTGTGCCAATTTCTGGCTGGAATGGTGACAACATGCTAGAACCAAGTGCTAATATGCTTATGGTCATGGGATGGAAAGTCACCCGTAAGGACGGCAATGCCAGTGGAACCACCCTGCTTGAAGCTCTGGATTGCATTCTGCCACCAACTCGCTCGCACTGACAAACGCTTGCGTTTGCCTCTCCAGGATGTCTATAAAATTGGTGGTATTGGTACTGTCCCTGTGGGTCGGGTGGAGACTGGTGTTCTCAAACCCGGCAGGTGGTCACCTTGCTCCAGTCAATGTAACAACTGAAGTGAAGTCTGTAGAAATGCACCATGAAGCATTGAGTGAAGCCCCTACCTGGGGACAATGTGGGCTTTAATGTCAAGAACGGTTCGTCAAAGATGTCTGTCATGGCAATGTGGTGGGTGACAGCAAAAATGATCCACCCATGGAAGCTGCTGGCTTCAAAGCTCAGGTGATTATTTAGAAACCATCCAGCCAAATCAGTGCTGGATATGCACCTGTGCTGGATTGTCACACAGCTCACATTGCTTGCAAGTTTGCTGAGCTAAAGGAGAAGATTGATCGGCTGCTCTGGGAAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAATCTGGTGACACTGCCATCGTTGATATGGTTCCTGGCAAGCCCATGTGTGTCGAGAGCCTCTGATTATCCTCCCCTGGGCCGTTTTGCTGTGCGTGACATGAGACAGATGTCGCTGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCAGTTGGAGCTGGCAAGGTCACCAAGTCTGCCCAGAAAGCCTGTATGCCAATGGTCATTATCCCCAATACCTGCCACCCCAGTCTTAATCAGTGGTGGAAGAACGGTCTCAGAACTGTTTGTCTCAATTGGCCATTTAAGTTTAATAGTAAAAGACTGGTTAATGATAACAATGCACGTAAACCTTCAGAAGGAAAGGAGAATGTTTTTGTGGACCATATGTTTTGTGTGTGGCAGTTTAAGTTATTAGTTTTTAAAATCAGTACTTTTTAATGAAAACAACTTGACCAAAAATCTGCTCACAGAATTTGAGACCCATTAAAAAAAGTTTAATGAGAAAAAAAAGAGAGATGG</td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                   </span></td><td>22</td><td> 37313899</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>RREB1    </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td>23</td><td><span style=white-space:pre-wrap>  4573369</span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td>26</td><td><span style=white-space:pre-wrap>  8583902</span></td><td><span style=white-space:pre-wrap>&lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>PLEKHS1  </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td>26</td><td> 32916345</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td>B3GALNT2 </td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                  </span></td><td>28</td><td><span style=white-space:pre-wrap>  8026290</span></td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>coding_sequence_variant&amp;feature_elongation                                                                 </span></td><td>29</td><td><span style=white-space:pre-wrap>   814496</span></td><td><span style=white-space:pre-wrap>GGGGTTCACCACCCCCCACCAGTACCACCCAGCCACAGGGACCCCAACCCCCAGGACCCACCACCACGGAGACCACCACCCCCACCAGTACCACAACCACTGGGACCCCTGCCTCAACACCTACAACC                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        </span></td><td>INS</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>         </span></td><td><span style=white-space:pre-wrap>stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                    </span></td><td>29</td><td> 46524877</td><td><span style=white-space:pre-wrap>N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </span></td><td>DEL</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 45 × 6\n",
       "\\begin{tabular}{r|llllll}\n",
       " SYMBOL & Consequence & CHROM & POS & ALT & SVTYPE\\\\\n",
       " <chr> & <chr> & <chr> & <int> & <chr> & <chr>\\\\\n",
       "\\hline\n",
       "\t ARHGEF10L & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                                    & 2  &   1406176 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&feature\\_truncation                                              & 2  & 109966395 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                               & 3  &  10637333 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                                    & 4  &   6744135 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t C7orf57   & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   & 4  & 112138554 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant                                                  & 5  &  27592200 & <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DUP\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                     & 5  &  58290107 & <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant                                                  & 5  & 101700700 & <INV>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & INV\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                               & 5  & 102381998 & <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DEL\\\\\n",
       "\t LMF2      & coding\\_sequence\\_variant\\&feature\\_elongation                                                                  & 5  & 119154005 & CCCCCCGCCGGCACGCCCGCCCCTCCGCGCCGGCCCCGCCCCGCCTCCGCGCCGGCCCCGCCCCG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & INS\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                     & 6  & 114481338 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&feature\\_elongation                                                                  & 7  &  41927433 & TGACAACTACCACCACTACTCCAAGAACAAGCACTACAAGAAGGACAACCACCACCACTAAAACCCCAAAGGACAACTACTACCACTACTCCAAGAAACAGCCACTACAAGAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & INS\\\\\n",
       "\t C5orf15   & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   & 7  &  65052970 & <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_elongation                                                   & 7  & 101977018 & <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DUP\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                     & 7  & 107999583 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t ACER2     & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   & 8  &  24574719 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                               & 9  &  15493182 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                     & 9  &  92049306 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant                                                  & 10 &  27366642 & <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DUP\\\\\n",
       "\t LYG1      & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   & 11 &   4319201 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation & 11 &  13759801 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&feature\\_elongation                                                                  & 12 &  73351320 & CGTTCTTTTTTTTTTTTTCTTTTTTTTTTCTTTCTTTTTTACTTTTATTTTATTTTTAAACTTTACATAATTGTATTAGTTTTGCCAAACATCAAAGTGAATCCACCACAGAGTATACATGTGTTCCCCATCCTGAACCCTCCTCCCTCCTCCCTCCCCATACCATCCCTCTGGAGTCGTCCCAATGCACTAGCTACAAGCATCCAGTATGAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & INS\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                     & 13 &  20646968 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant                              & 13 &  20906813 & <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DUP\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                & 13 &  25258768 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation & 13 &  77550072 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t DCHS1     & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant                              & 15 &  46356965 & <INV>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & INV\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                     & 15 &  49323433 & <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DEL\\\\\n",
       "\t USH2A     & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   & 16 &  18381410 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t WSCD2     & coding\\_sequence\\_variant\\&feature\\_elongation                                                                  & 17 &  64326523 & TGTTGGGGGCCAGAGTGAGGTACTCCGCCCATGGCAAGGTCATGAGGAAGGAGGCTCGGCTATCGCAAGTGAGGATCAGGCCTCAGGAGTCCCTAAATCCTCGGCGTCTACCCATAACCAGAGCCTGCCTACTTTACTACTTTGTGCTCTTACCTACACCTCCTGACTTTACGGGGCTGTCCCCACCCTCTTCGGAGAAGGAGTTAACCTAGAGCTCAGTCAATAAAAACTCTTGGGTGTGGCAAGAGTGTTTTAACCACTACAAACTCCTCTGAAGGTTCTCTGGCCCTGCCCTGACAGGCTCGTCCGGCCACATGTGAGTTGCTCGCAGCCTCCCAACCATGAGCTGAGATGCTTTGACCTTCACAAAAACAGGTTCCTTAGAAAAGTTAGAAAACTATTAGTATAAGTATAATGGGCCTAATTAGAAATTGTGTTGGTGAAGGGGTTTTTCATTTGCTGAGCCAATGTTTGTTGCTAAGTCTCATATCCTGCCACTTACACGTGTGAATATATAGAATTGACCTTTGATATTAATCACGTTAGACCTTAGGCTAAACCAAATTCTTTCCTTAACTAAAACCCACTACACCTCACCTGTAGGAGTGTAACTTTACTTAGGTGGCGTCTGTTTTGAGAATAATCAGCCCTGGAGAAATAAGTGTGTCCTGATTGACTGACCGCTGTCACAAAGGGAGAGGAGTAAATAAATTGTCAGCAGGCCCCCTGGCCCAGAGATGATGTAACACCCCTAAGACCTCTGTATACATTTTGTGTGAAGCACCTGACTTTAATAAAGTCAGGACTGCTGTCCCCACGTGACTTTTGTATAACATCTTAGTGTATAAAAACAGACTCTGGAAAATAAAAAATTTGGGGATCAGTTTCTCAAAATACTGGTCTCCCCATGTCTCTCTCTCCCTCGGCTGAGTCTCCATCTGGAGGCGCAGGAACCCGCAAGCTTACTAATTTTGCCTGGGCTTCTAGATCCGACCGGGAGGCCTCAGTGTCTCCTCTCCTTCGGGAGAGCGGAAGGACGATACAAACCTACGTAAGTGATGCAAGCTTCTTGTCTTGAAGTTTTGTGGTCCCAACGTAAACCAAGCTACTCGGCCTCTTTTCTCCACTGAATTTTCCTACTGAGCTATCGCACTTATTCTAGTACTCTTTATATCTCTAATTAATATCTATTGAAACTATACGTATCTGACCCTCGCCCGATGCCGTCTCTCGCCAGTACCCTGGATCGGCAGGGCTGGTCCTGGGTT                                                     & INS\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&feature\\_elongation                                                                  & 17 &  71655478 & TCCTTCCTCCTCCGCCGCCCTCCGCCCCACCTCCTCCCCCTGCCGCCCCCTCCCGCCCCACCTCCTCGCCGCCCCTCCGCCCCT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     & INS\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                               & 18 &    699541 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation & 18 &   4687966 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant                                                                 & 18 &  18071065 & <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DUP\\\\\n",
       "\t ADGRG5    & coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant                                                  & 18 &  33328933 & N{[}19:38711484{[}                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & TRA\\\\\n",
       "\t STX8      & coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&feature\\_truncation                                              & 19 &  28840835 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&5\\_prime\\_UTR\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                & 20 &  25550031 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&feature\\_elongation                                                                  & 22 &  16418735 & AATTCTGAAGCCGGTATCTCCAAGAACGGGCAGACCCGTGAGCATGCTCCTTCTGTCTTACACCCTGGGTGTGAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCACCCTATAGCCAGAAGAGATACGAAGAAATTGTTAAGGAAGCCAGCACCTACATTAAGAAATTGGCTACAACCCCCACACGGTAGCATTTGTGCCAATTTCTGGCTGGAATGGTGACAACATGCTAGAACCAAGTGCTAATATGCTTATGGTCATGGGATGGAAAGTCACCCGTAAGGACGGCAATGCCAGTGGAACCACCCTGCTTGAAGCTCTGGATTGCATTCTGCCACCAACTCGCTCGCACTGACAAACGCTTGCGTTTGCCTCTCCAGGATGTCTATAAAATTGGTGGTATTGGTACTGTCCCTGTGGGTCGGGTGGAGACTGGTGTTCTCAAACCCGGCAGGTGGTCACCTTGCTCCAGTCAATGTAACAACTGAAGTGAAGTCTGTAGAAATGCACCATGAAGCATTGAGTGAAGCCCCTACCTGGGGACAATGTGGGCTTTAATGTCAAGAACGGTTCGTCAAAGATGTCTGTCATGGCAATGTGGTGGGTGACAGCAAAAATGATCCACCCATGGAAGCTGCTGGCTTCAAAGCTCAGGTGATTATTTAGAAACCATCCAGCCAAATCAGTGCTGGATATGCACCTGTGCTGGATTGTCACACAGCTCACATTGCTTGCAAGTTTGCTGAGCTAAAGGAGAAGATTGATCGGCTGCTCTGGGAAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAATCTGGTGACACTGCCATCGTTGATATGGTTCCTGGCAAGCCCATGTGTGTCGAGAGCCTCTGATTATCCTCCCCTGGGCCGTTTTGCTGTGCGTGACATGAGACAGATGTCGCTGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCAGTTGGAGCTGGCAAGGTCACCAAGTCTGCCCAGAAAGCCTGTATGCCAATGGTCATTATCCCCAATACCTGCCACCCCAGTCTTAATCAGTGGTGGAAGAACGGTCTCAGAACTGTTTGTCTCAATTGGCCATTTAAGTTTAATAGTAAAAGACTGGTTAATGATAACAATGCACGTAAACCTTCAGAAGGAAAGGAGAATGTTTTTGTGGACCATATGTTTTGTGTGTGGCAGTTTAAGTTATTAGTTTTTAAAATCAGTACTTTTTAATGAAAACAACTTGACCAAAAATCTGCTCACAGAATTTGAGACCCATTAAAAAAAGTTTAATGAGAAAAAAAAGAGAGATGG & INS\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&feature\\_truncation                                    & 22 &  37313899 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t RREB1     & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   & 23 &   4573369 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   & 26 &   8583902 & <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & DEL\\\\\n",
       "\t PLEKHS1   & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   & 26 &  32916345 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t B3GALNT2  & coding\\_sequence\\_variant\\&intron\\_variant\\&feature\\_truncation                                                   & 28 &   8026290 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\t           & coding\\_sequence\\_variant\\&feature\\_elongation                                                                  & 29 &    814496 & GGGGTTCACCACCCCCCACCAGTACCACCCAGCCACAGGGACCCCAACCCCCAGGACCCACCACCACGGAGACCACCACCCCCACCAGTACCACAACCACTGGGACCCCTGCCTCAACACCTACAACC                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         & INS\\\\\n",
       "\t           & stop\\_lost\\&coding\\_sequence\\_variant\\&3\\_prime\\_UTR\\_variant\\&intron\\_variant\\&feature\\_truncation                     & 29 &  46524877 & N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & DEL\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 45 × 6\n",
       "\n",
       "| SYMBOL &lt;chr&gt; | Consequence &lt;chr&gt; | CHROM &lt;chr&gt; | POS &lt;int&gt; | ALT &lt;chr&gt; | SVTYPE &lt;chr&gt; |\n",
       "|---|---|---|---|---|---|\n",
       "| ARHGEF10L | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                    | 2  |   1406176 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                              | 2  | 109966395 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                               | 3  |  10637333 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                    | 4  |   6744135 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| C7orf57   | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   | 4  | 112138554 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                                  | 5  |  27592200 | &lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DUP |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     | 5  |  58290107 | &lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant                                                  | 5  | 101700700 | &lt;INV&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | INV |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                               | 5  | 102381998 | &lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DEL |\n",
       "| LMF2      | coding_sequence_variant&amp;feature_elongation                                                                  | 5  | 119154005 | CCCCCCGCCGGCACGCCCGCCCCTCCGCGCCGGCCCCGCCCCGCCTCCGCGCCGGCCCCGCCCCG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | INS |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     | 6  | 114481338 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                                  | 7  |  41927433 | TGACAACTACCACCACTACTCCAAGAACAAGCACTACAAGAAGGACAACCACCACCACTAAAACCCCAAAGGACAACTACTACCACTACTCCAAGAAACAGCCACTACAAGAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | INS |\n",
       "| C5orf15   | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   | 7  |  65052970 | &lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;intron_variant&amp;feature_elongation                                                   | 7  | 101977018 | &lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DUP |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     | 7  | 107999583 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| ACER2     | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   | 8  |  24574719 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                               | 9  |  15493182 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     | 9  |  92049306 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant                                                  | 10 |  27366642 | &lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DUP |\n",
       "| LYG1      | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   | 11 |   4319201 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation | 11 |  13759801 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                                  | 12 |  73351320 | CGTTCTTTTTTTTTTTTTCTTTTTTTTTTCTTTCTTTTTTACTTTTATTTTATTTTTAAACTTTACATAATTGTATTAGTTTTGCCAAACATCAAAGTGAATCCACCACAGAGTATACATGTGTTCCCCATCCTGAACCCTCCTCCCTCCTCCCTCCCCATACCATCCCTCTGGAGTCGTCCCAATGCACTAGCTACAAGCATCCAGTATGAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | INS |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     | 13 |  20646968 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant                              | 13 |  20906813 | &lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DUP |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation                | 13 |  25258768 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation | 13 |  77550072 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| DCHS1     | coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant                              | 15 |  46356965 | &lt;INV&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | INV |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     | 15 |  49323433 | &lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DEL |\n",
       "| USH2A     | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   | 16 |  18381410 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| WSCD2     | coding_sequence_variant&amp;feature_elongation                                                                  | 17 |  64326523 | TGTTGGGGGCCAGAGTGAGGTACTCCGCCCATGGCAAGGTCATGAGGAAGGAGGCTCGGCTATCGCAAGTGAGGATCAGGCCTCAGGAGTCCCTAAATCCTCGGCGTCTACCCATAACCAGAGCCTGCCTACTTTACTACTTTGTGCTCTTACCTACACCTCCTGACTTTACGGGGCTGTCCCCACCCTCTTCGGAGAAGGAGTTAACCTAGAGCTCAGTCAATAAAAACTCTTGGGTGTGGCAAGAGTGTTTTAACCACTACAAACTCCTCTGAAGGTTCTCTGGCCCTGCCCTGACAGGCTCGTCCGGCCACATGTGAGTTGCTCGCAGCCTCCCAACCATGAGCTGAGATGCTTTGACCTTCACAAAAACAGGTTCCTTAGAAAAGTTAGAAAACTATTAGTATAAGTATAATGGGCCTAATTAGAAATTGTGTTGGTGAAGGGGTTTTTCATTTGCTGAGCCAATGTTTGTTGCTAAGTCTCATATCCTGCCACTTACACGTGTGAATATATAGAATTGACCTTTGATATTAATCACGTTAGACCTTAGGCTAAACCAAATTCTTTCCTTAACTAAAACCCACTACACCTCACCTGTAGGAGTGTAACTTTACTTAGGTGGCGTCTGTTTTGAGAATAATCAGCCCTGGAGAAATAAGTGTGTCCTGATTGACTGACCGCTGTCACAAAGGGAGAGGAGTAAATAAATTGTCAGCAGGCCCCCTGGCCCAGAGATGATGTAACACCCCTAAGACCTCTGTATACATTTTGTGTGAAGCACCTGACTTTAATAAAGTCAGGACTGCTGTCCCCACGTGACTTTTGTATAACATCTTAGTGTATAAAAACAGACTCTGGAAAATAAAAAATTTGGGGATCAGTTTCTCAAAATACTGGTCTCCCCATGTCTCTCTCTCCCTCGGCTGAGTCTCCATCTGGAGGCGCAGGAACCCGCAAGCTTACTAATTTTGCCTGGGCTTCTAGATCCGACCGGGAGGCCTCAGTGTCTCCTCTCCTTCGGGAGAGCGGAAGGACGATACAAACCTACGTAAGTGATGCAAGCTTCTTGTCTTGAAGTTTTGTGGTCCCAACGTAAACCAAGCTACTCGGCCTCTTTTCTCCACTGAATTTTCCTACTGAGCTATCGCACTTATTCTAGTACTCTTTATATCTCTAATTAATATCTATTGAAACTATACGTATCTGACCCTCGCCCGATGCCGTCTCTCGCCAGTACCCTGGATCGGCAGGGCTGGTCCTGGGTT                                                     | INS |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                                  | 17 |  71655478 | TCCTTCCTCCTCCGCCGCCCTCCGCCCCACCTCCTCCCCCTGCCGCCCCCTCCCGCCCCACCTCCTCGCCGCCCCTCCGCCCCT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | INS |\n",
       "| <!----> | coding_sequence_variant&amp;5_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                               | 18 |    699541 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation | 18 |   4687966 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;3_prime_UTR_variant                                                                 | 18 |  18071065 | &lt;DUP&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DUP |\n",
       "| ADGRG5    | coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant                                                  | 18 |  33328933 | N[19:38711484[                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | TRA |\n",
       "| STX8      | coding_sequence_variant&amp;5_prime_UTR_variant&amp;feature_truncation                                              | 19 |  28840835 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;5_prime_UTR_variant&amp;3_prime_UTR_variant&amp;feature_truncation                | 20 |  25550031 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                                  | 22 |  16418735 | AATTCTGAAGCCGGTATCTCCAAGAACGGGCAGACCCGTGAGCATGCTCCTTCTGTCTTACACCCTGGGTGTGAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCACCCTATAGCCAGAAGAGATACGAAGAAATTGTTAAGGAAGCCAGCACCTACATTAAGAAATTGGCTACAACCCCCACACGGTAGCATTTGTGCCAATTTCTGGCTGGAATGGTGACAACATGCTAGAACCAAGTGCTAATATGCTTATGGTCATGGGATGGAAAGTCACCCGTAAGGACGGCAATGCCAGTGGAACCACCCTGCTTGAAGCTCTGGATTGCATTCTGCCACCAACTCGCTCGCACTGACAAACGCTTGCGTTTGCCTCTCCAGGATGTCTATAAAATTGGTGGTATTGGTACTGTCCCTGTGGGTCGGGTGGAGACTGGTGTTCTCAAACCCGGCAGGTGGTCACCTTGCTCCAGTCAATGTAACAACTGAAGTGAAGTCTGTAGAAATGCACCATGAAGCATTGAGTGAAGCCCCTACCTGGGGACAATGTGGGCTTTAATGTCAAGAACGGTTCGTCAAAGATGTCTGTCATGGCAATGTGGTGGGTGACAGCAAAAATGATCCACCCATGGAAGCTGCTGGCTTCAAAGCTCAGGTGATTATTTAGAAACCATCCAGCCAAATCAGTGCTGGATATGCACCTGTGCTGGATTGTCACACAGCTCACATTGCTTGCAAGTTTGCTGAGCTAAAGGAGAAGATTGATCGGCTGCTCTGGGAAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAATCTGGTGACACTGCCATCGTTGATATGGTTCCTGGCAAGCCCATGTGTGTCGAGAGCCTCTGATTATCCTCCCCTGGGCCGTTTTGCTGTGCGTGACATGAGACAGATGTCGCTGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCAGTTGGAGCTGGCAAGGTCACCAAGTCTGCCCAGAAAGCCTGTATGCCAATGGTCATTATCCCCAATACCTGCCACCCCAGTCTTAATCAGTGGTGGAAGAACGGTCTCAGAACTGTTTGTCTCAATTGGCCATTTAAGTTTAATAGTAAAAGACTGGTTAATGATAACAATGCACGTAAACCTTCAGAAGGAAAGGAGAATGTTTTTGTGGACCATATGTTTTGTGTGTGGCAGTTTAAGTTATTAGTTTTTAAAATCAGTACTTTTTAATGAAAACAACTTGACCAAAAATCTGCTCACAGAATTTGAGACCCATTAAAAAAAGTTTAATGAGAAAAAAAAGAGAGATGG | INS |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;feature_truncation                                    | 22 |  37313899 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| RREB1     | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   | 23 |   4573369 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   | 26 |   8583902 | &lt;DEL&gt;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | DEL |\n",
       "| PLEKHS1   | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   | 26 |  32916345 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| B3GALNT2  | coding_sequence_variant&amp;intron_variant&amp;feature_truncation                                                   | 28 |   8026290 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "| <!----> | coding_sequence_variant&amp;feature_elongation                                                                  | 29 |    814496 | GGGGTTCACCACCCCCCACCAGTACCACCCAGCCACAGGGACCCCAACCCCCAGGACCCACCACCACGGAGACCACCACCCCCACCAGTACCACAACCACTGGGACCCCTGCCTCAACACCTACAACC                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | INS |\n",
       "| <!----> | stop_lost&amp;coding_sequence_variant&amp;3_prime_UTR_variant&amp;intron_variant&amp;feature_truncation                     | 29 |  46524877 | N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | DEL |\n",
       "\n"
      ],
      "text/plain": [
       "   SYMBOL   \n",
       "1  ARHGEF10L\n",
       "2           \n",
       "3           \n",
       "4           \n",
       "5  C7orf57  \n",
       "6           \n",
       "7           \n",
       "8           \n",
       "9           \n",
       "10 LMF2     \n",
       "11          \n",
       "12          \n",
       "13 C5orf15  \n",
       "14          \n",
       "15          \n",
       "16 ACER2    \n",
       "17          \n",
       "18          \n",
       "19          \n",
       "20 LYG1     \n",
       "21          \n",
       "22          \n",
       "23          \n",
       "24          \n",
       "25          \n",
       "26          \n",
       "27 DCHS1    \n",
       "28          \n",
       "29 USH2A    \n",
       "30 WSCD2    \n",
       "31          \n",
       "32          \n",
       "33          \n",
       "34          \n",
       "35 ADGRG5   \n",
       "36 STX8     \n",
       "37          \n",
       "38          \n",
       "39          \n",
       "40 RREB1    \n",
       "41          \n",
       "42 PLEKHS1  \n",
       "43 B3GALNT2 \n",
       "44          \n",
       "45          \n",
       "   Consequence                                                                                                \n",
       "1  stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                                   \n",
       "2  coding_sequence_variant&5_prime_UTR_variant&feature_truncation                                             \n",
       "3  coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation                              \n",
       "4  stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                                   \n",
       "5  coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "6  coding_sequence_variant&5_prime_UTR_variant&intron_variant                                                 \n",
       "7  stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "8  coding_sequence_variant&3_prime_UTR_variant&intron_variant                                                 \n",
       "9  coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation                              \n",
       "10 coding_sequence_variant&feature_elongation                                                                 \n",
       "11 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "12 coding_sequence_variant&feature_elongation                                                                 \n",
       "13 coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "14 coding_sequence_variant&intron_variant&feature_elongation                                                  \n",
       "15 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "16 coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "17 coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation                              \n",
       "18 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "19 coding_sequence_variant&5_prime_UTR_variant&intron_variant                                                 \n",
       "20 coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "21 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant&feature_truncation\n",
       "22 coding_sequence_variant&feature_elongation                                                                 \n",
       "23 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "24 coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant                             \n",
       "25 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation               \n",
       "26 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant&feature_truncation\n",
       "27 coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant                             \n",
       "28 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "29 coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "30 coding_sequence_variant&feature_elongation                                                                 \n",
       "31 coding_sequence_variant&feature_elongation                                                                 \n",
       "32 coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation                              \n",
       "33 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&intron_variant&feature_truncation\n",
       "34 coding_sequence_variant&3_prime_UTR_variant                                                                \n",
       "35 coding_sequence_variant&3_prime_UTR_variant&intron_variant                                                 \n",
       "36 coding_sequence_variant&5_prime_UTR_variant&feature_truncation                                             \n",
       "37 stop_lost&coding_sequence_variant&5_prime_UTR_variant&3_prime_UTR_variant&feature_truncation               \n",
       "38 coding_sequence_variant&feature_elongation                                                                 \n",
       "39 stop_lost&coding_sequence_variant&3_prime_UTR_variant&feature_truncation                                   \n",
       "40 coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "41 coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "42 coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "43 coding_sequence_variant&intron_variant&feature_truncation                                                  \n",
       "44 coding_sequence_variant&feature_elongation                                                                 \n",
       "45 stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation                    \n",
       "   CHROM POS      \n",
       "1  2       1406176\n",
       "2  2     109966395\n",
       "3  3      10637333\n",
       "4  4       6744135\n",
       "5  4     112138554\n",
       "6  5      27592200\n",
       "7  5      58290107\n",
       "8  5     101700700\n",
       "9  5     102381998\n",
       "10 5     119154005\n",
       "11 6     114481338\n",
       "12 7      41927433\n",
       "13 7      65052970\n",
       "14 7     101977018\n",
       "15 7     107999583\n",
       "16 8      24574719\n",
       "17 9      15493182\n",
       "18 9      92049306\n",
       "19 10     27366642\n",
       "20 11      4319201\n",
       "21 11     13759801\n",
       "22 12     73351320\n",
       "23 13     20646968\n",
       "24 13     20906813\n",
       "25 13     25258768\n",
       "26 13     77550072\n",
       "27 15     46356965\n",
       "28 15     49323433\n",
       "29 16     18381410\n",
       "30 17     64326523\n",
       "31 17     71655478\n",
       "32 18       699541\n",
       "33 18      4687966\n",
       "34 18     18071065\n",
       "35 18     33328933\n",
       "36 19     28840835\n",
       "37 20     25550031\n",
       "38 22     16418735\n",
       "39 22     37313899\n",
       "40 23      4573369\n",
       "41 26      8583902\n",
       "42 26     32916345\n",
       "43 28      8026290\n",
       "44 29       814496\n",
       "45 29     46524877\n",
       "   ALT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     \n",
       "1  N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "2  N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "3  N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "4  N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "5  N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "6  <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "7  <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "8  <INV>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "9  <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "10 CCCCCCGCCGGCACGCCCGCCCCTCCGCGCCGGCCCCGCCCCGCCTCCGCGCCGGCCCCGCCCCG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "11 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "12 TGACAACTACCACCACTACTCCAAGAACAAGCACTACAAGAAGGACAACCACCACCACTAAAACCCCAAAGGACAACTACTACCACTACTCCAAGAAACAGCCACTACAAGAA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "13 <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "14 <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "15 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "16 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "17 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "18 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "19 <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "20 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "21 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "22 CGTTCTTTTTTTTTTTTTCTTTTTTTTTTCTTTCTTTTTTACTTTTATTTTATTTTTAAACTTTACATAATTGTATTAGTTTTGCCAAACATCAAAGTGAATCCACCACAGAGTATACATGTGTTCCCCATCCTGAACCCTCCTCCCTCCTCCCTCCCCATACCATCCCTCTGGAGTCGTCCCAATGCACTAGCTACAAGCATCCAGTATGAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "23 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "24 <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "25 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "26 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "27 <INV>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "28 <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "29 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "30 TGTTGGGGGCCAGAGTGAGGTACTCCGCCCATGGCAAGGTCATGAGGAAGGAGGCTCGGCTATCGCAAGTGAGGATCAGGCCTCAGGAGTCCCTAAATCCTCGGCGTCTACCCATAACCAGAGCCTGCCTACTTTACTACTTTGTGCTCTTACCTACACCTCCTGACTTTACGGGGCTGTCCCCACCCTCTTCGGAGAAGGAGTTAACCTAGAGCTCAGTCAATAAAAACTCTTGGGTGTGGCAAGAGTGTTTTAACCACTACAAACTCCTCTGAAGGTTCTCTGGCCCTGCCCTGACAGGCTCGTCCGGCCACATGTGAGTTGCTCGCAGCCTCCCAACCATGAGCTGAGATGCTTTGACCTTCACAAAAACAGGTTCCTTAGAAAAGTTAGAAAACTATTAGTATAAGTATAATGGGCCTAATTAGAAATTGTGTTGGTGAAGGGGTTTTTCATTTGCTGAGCCAATGTTTGTTGCTAAGTCTCATATCCTGCCACTTACACGTGTGAATATATAGAATTGACCTTTGATATTAATCACGTTAGACCTTAGGCTAAACCAAATTCTTTCCTTAACTAAAACCCACTACACCTCACCTGTAGGAGTGTAACTTTACTTAGGTGGCGTCTGTTTTGAGAATAATCAGCCCTGGAGAAATAAGTGTGTCCTGATTGACTGACCGCTGTCACAAAGGGAGAGGAGTAAATAAATTGTCAGCAGGCCCCCTGGCCCAGAGATGATGTAACACCCCTAAGACCTCTGTATACATTTTGTGTGAAGCACCTGACTTTAATAAAGTCAGGACTGCTGTCCCCACGTGACTTTTGTATAACATCTTAGTGTATAAAAACAGACTCTGGAAAATAAAAAATTTGGGGATCAGTTTCTCAAAATACTGGTCTCCCCATGTCTCTCTCTCCCTCGGCTGAGTCTCCATCTGGAGGCGCAGGAACCCGCAAGCTTACTAATTTTGCCTGGGCTTCTAGATCCGACCGGGAGGCCTCAGTGTCTCCTCTCCTTCGGGAGAGCGGAAGGACGATACAAACCTACGTAAGTGATGCAAGCTTCTTGTCTTGAAGTTTTGTGGTCCCAACGTAAACCAAGCTACTCGGCCTCTTTTCTCCACTGAATTTTCCTACTGAGCTATCGCACTTATTCTAGTACTCTTTATATCTCTAATTAATATCTATTGAAACTATACGTATCTGACCCTCGCCCGATGCCGTCTCTCGCCAGTACCCTGGATCGGCAGGGCTGGTCCTGGGTT                                                    \n",
       "31 TCCTTCCTCCTCCGCCGCCCTCCGCCCCACCTCCTCCCCCTGCCGCCCCCTCCCGCCCCACCTCCTCGCCGCCCCTCCGCCCCT                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    \n",
       "32 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "33 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "34 <DUP>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "35 N[19:38711484[                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "36 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "37 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "38 AATTCTGAAGCCGGTATCTCCAAGAACGGGCAGACCCGTGAGCATGCTCCTTCTGTCTTACACCCTGGGTGTGAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCACCCTATAGCCAGAAGAGATACGAAGAAATTGTTAAGGAAGCCAGCACCTACATTAAGAAATTGGCTACAACCCCCACACGGTAGCATTTGTGCCAATTTCTGGCTGGAATGGTGACAACATGCTAGAACCAAGTGCTAATATGCTTATGGTCATGGGATGGAAAGTCACCCGTAAGGACGGCAATGCCAGTGGAACCACCCTGCTTGAAGCTCTGGATTGCATTCTGCCACCAACTCGCTCGCACTGACAAACGCTTGCGTTTGCCTCTCCAGGATGTCTATAAAATTGGTGGTATTGGTACTGTCCCTGTGGGTCGGGTGGAGACTGGTGTTCTCAAACCCGGCAGGTGGTCACCTTGCTCCAGTCAATGTAACAACTGAAGTGAAGTCTGTAGAAATGCACCATGAAGCATTGAGTGAAGCCCCTACCTGGGGACAATGTGGGCTTTAATGTCAAGAACGGTTCGTCAAAGATGTCTGTCATGGCAATGTGGTGGGTGACAGCAAAAATGATCCACCCATGGAAGCTGCTGGCTTCAAAGCTCAGGTGATTATTTAGAAACCATCCAGCCAAATCAGTGCTGGATATGCACCTGTGCTGGATTGTCACACAGCTCACATTGCTTGCAAGTTTGCTGAGCTAAAGGAGAAGATTGATCGGCTGCTCTGGGAAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAATCTGGTGACACTGCCATCGTTGATATGGTTCCTGGCAAGCCCATGTGTGTCGAGAGCCTCTGATTATCCTCCCCTGGGCCGTTTTGCTGTGCGTGACATGAGACAGATGTCGCTGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCAGTTGGAGCTGGCAAGGTCACCAAGTCTGCCCAGAAAGCCTGTATGCCAATGGTCATTATCCCCAATACCTGCCACCCCAGTCTTAATCAGTGGTGGAAGAACGGTCTCAGAACTGTTTGTCTCAATTGGCCATTTAAGTTTAATAGTAAAAGACTGGTTAATGATAACAATGCACGTAAACCTTCAGAAGGAAAGGAGAATGTTTTTGTGGACCATATGTTTTGTGTGTGGCAGTTTAAGTTATTAGTTTTTAAAATCAGTACTTTTTAATGAAAACAACTTGACCAAAAATCTGCTCACAGAATTTGAGACCCATTAAAAAAAGTTTAATGAGAAAAAAAAGAGAGATGG\n",
       "39 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "40 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "41 <DEL>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   \n",
       "42 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "43 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "44 GGGGTTCACCACCCCCCACCAGTACCACCCAGCCACAGGGACCCCAACCCCCAGGACCCACCACCACGGAGACCACCACCCCCACCAGTACCACAACCACTGGGACCCCTGCCTCAACACCTACAACC                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        \n",
       "45 N                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       \n",
       "   SVTYPE\n",
       "1  DEL   \n",
       "2  DEL   \n",
       "3  DEL   \n",
       "4  DEL   \n",
       "5  DEL   \n",
       "6  DUP   \n",
       "7  DEL   \n",
       "8  INV   \n",
       "9  DEL   \n",
       "10 INS   \n",
       "11 DEL   \n",
       "12 INS   \n",
       "13 DEL   \n",
       "14 DUP   \n",
       "15 DEL   \n",
       "16 DEL   \n",
       "17 DEL   \n",
       "18 DEL   \n",
       "19 DUP   \n",
       "20 DEL   \n",
       "21 DEL   \n",
       "22 INS   \n",
       "23 DEL   \n",
       "24 DUP   \n",
       "25 DEL   \n",
       "26 DEL   \n",
       "27 INV   \n",
       "28 DEL   \n",
       "29 DEL   \n",
       "30 INS   \n",
       "31 INS   \n",
       "32 DEL   \n",
       "33 DEL   \n",
       "34 DUP   \n",
       "35 TRA   \n",
       "36 DEL   \n",
       "37 DEL   \n",
       "38 INS   \n",
       "39 DEL   \n",
       "40 DEL   \n",
       "41 DEL   \n",
       "42 DEL   \n",
       "43 DEL   \n",
       "44 INS   \n",
       "45 DEL   "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "auto_UCD[Consequence %like%'coding_sequence_variant',c('SYMBOL','Consequence','CHROM','POS','ALT','SVTYPE')]\n",
    "auto_angus[Consequence%like%'coding_sequence_variant',c('SYMBOL','Consequence','CHROM','POS','ALT','SVTYPE')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 320 × 5</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SYMBOL</th><th scope=col>Consequence</th><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ALT</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td><span style=white-space:pre-wrap>  1275339</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>PLCL2   </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td><span style=white-space:pre-wrap>  3367537</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td><span style=white-space:pre-wrap>  4427304</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td><span style=white-space:pre-wrap>  7152053</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td> 13267717</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 25477750</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 47529708</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 53236659</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>NAALADL2</td><td>intron_variant&amp;feature_elongation</td><td>1</td><td> 64894887</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 75759547</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>KALRN   </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td> 88453220</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>ARHGAP31</td><td><span style=white-space:pre-wrap>downstream_gene_variant          </span></td><td>1</td><td> 92862060</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>108437988</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>IMPG2   </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td>111440634</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>CADM2   </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td>123408453</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>125180056</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>127337009</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>153345553</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>PADI2   </span></td><td>intron_variant&amp;feature_elongation</td><td>2</td><td><span style=white-space:pre-wrap>   896085</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td><span style=white-space:pre-wrap>  1619392</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td><span style=white-space:pre-wrap>  3886512</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td> 14553628</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>SERPINE2</td><td>intron_variant&amp;feature_elongation</td><td>2</td><td> 24032585</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td> 38098417</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>ACADL   </span></td><td>intron_variant&amp;feature_elongation</td><td>2</td><td> 38164553</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>ADAM23  </span></td><td>intron_variant&amp;feature_elongation</td><td>2</td><td> 41389000</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td> 67430957</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>DPP10   </span></td><td>intron_variant&amp;feature_elongation</td><td>2</td><td> 69421935</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>TLK1    </span></td><td>intron_variant&amp;feature_elongation</td><td>2</td><td>108752602</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td>113455429</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>FANK1  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>26</td><td>44066920</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>26</td><td>48562031</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>INPP5A </td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>26</td><td>49863932</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>downstream_gene_variant                                        </span></td><td>26</td><td>50306469</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>ECHS1  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>26</td><td>50374695</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td>intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation</td><td>27</td><td> 9577172</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>27</td><td>11197279</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>PRIMPOL</td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>27</td><td>14197236</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>UNC5D  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>27</td><td>30293910</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>27</td><td>33865263</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>27</td><td>41976031</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>27</td><td>42276554</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td>intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation</td><td>27</td><td>43037771</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>SIPA1L2</td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>28</td><td> 5544508</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>upstream_gene_variant                                          </span></td><td>28</td><td> 7748550</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>28</td><td> 7912357</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>28</td><td> 8881602</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>CTNNA3 </td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>28</td><td>22086810</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td>intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation</td><td>28</td><td>26908422</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>ASCC1  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>28</td><td>28022819</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>29</td><td> 1199982</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>CARS1  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>29</td><td> 2560092</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>SHANK2 </td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>29</td><td> 3070186</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>upstream_gene_variant                                          </span></td><td>29</td><td> 3758853</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>29</td><td> 7216770</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>29</td><td>18929786</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>29</td><td>20060164</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>upstream_gene_variant                                          </span></td><td>29</td><td>23204937</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>PRCP   </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>29</td><td>38556044</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>29</td><td>42620542</td><td>&lt;DUP&gt;</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 320 × 5\n",
       "\\begin{tabular}{r|lllll}\n",
       " SYMBOL & Consequence & CHROM & POS & ALT\\\\\n",
       " <chr> & <chr> & <chr> & <int> & <chr>\\\\\n",
       "\\hline\n",
       "\t          & intergenic\\_variant                & 1 &   1275339 & <DUP>\\\\\n",
       "\t PLCL2    & intron\\_variant\\&feature\\_elongation & 1 &   3367537 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &   4427304 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &   7152053 & <DUP>\\\\\n",
       "\t          & intron\\_variant\\&feature\\_elongation & 1 &  13267717 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  25477750 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  47529708 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  53236659 & <DUP>\\\\\n",
       "\t NAALADL2 & intron\\_variant\\&feature\\_elongation & 1 &  64894887 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  75759547 & <DUP>\\\\\n",
       "\t KALRN    & intron\\_variant\\&feature\\_elongation & 1 &  88453220 & <DUP>\\\\\n",
       "\t ARHGAP31 & downstream\\_gene\\_variant           & 1 &  92862060 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 108437988 & <DUP>\\\\\n",
       "\t IMPG2    & intron\\_variant\\&feature\\_elongation & 1 & 111440634 & <DUP>\\\\\n",
       "\t CADM2    & intron\\_variant\\&feature\\_elongation & 1 & 123408453 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 125180056 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 127337009 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 153345553 & <DUP>\\\\\n",
       "\t PADI2    & intron\\_variant\\&feature\\_elongation & 2 &    896085 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 &   1619392 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 &   3886512 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 &  14553628 & <DUP>\\\\\n",
       "\t SERPINE2 & intron\\_variant\\&feature\\_elongation & 2 &  24032585 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 &  38098417 & <DUP>\\\\\n",
       "\t ACADL    & intron\\_variant\\&feature\\_elongation & 2 &  38164553 & <DUP>\\\\\n",
       "\t ADAM23   & intron\\_variant\\&feature\\_elongation & 2 &  41389000 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 &  67430957 & <DUP>\\\\\n",
       "\t DPP10    & intron\\_variant\\&feature\\_elongation & 2 &  69421935 & <DUP>\\\\\n",
       "\t TLK1     & intron\\_variant\\&feature\\_elongation & 2 & 108752602 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 & 113455429 & <DUP>\\\\\n",
       "\t ⋮ & ⋮ & ⋮ & ⋮ & ⋮\\\\\n",
       "\t FANK1   & intron\\_variant\\&feature\\_elongation                               & 26 & 44066920 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 26 & 48562031 & <DUP>\\\\\n",
       "\t INPP5A  & intron\\_variant\\&feature\\_elongation                               & 26 & 49863932 & <DUP>\\\\\n",
       "\t         & downstream\\_gene\\_variant                                         & 26 & 50306469 & <DUP>\\\\\n",
       "\t ECHS1   & intron\\_variant\\&feature\\_elongation                               & 26 & 50374695 & <DUP>\\\\\n",
       "\t         & intron\\_variant\\&non\\_coding\\_transcript\\_variant\\&feature\\_elongation & 27 &  9577172 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 27 & 11197279 & <DUP>\\\\\n",
       "\t PRIMPOL & intron\\_variant\\&feature\\_elongation                               & 27 & 14197236 & <DUP>\\\\\n",
       "\t UNC5D   & intron\\_variant\\&feature\\_elongation                               & 27 & 30293910 & <DUP>\\\\\n",
       "\t         & intron\\_variant\\&feature\\_elongation                               & 27 & 33865263 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 27 & 41976031 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 27 & 42276554 & <DUP>\\\\\n",
       "\t         & intron\\_variant\\&non\\_coding\\_transcript\\_variant\\&feature\\_elongation & 27 & 43037771 & <DUP>\\\\\n",
       "\t SIPA1L2 & intron\\_variant\\&feature\\_elongation                               & 28 &  5544508 & <DUP>\\\\\n",
       "\t         & upstream\\_gene\\_variant                                           & 28 &  7748550 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 28 &  7912357 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 28 &  8881602 & <DUP>\\\\\n",
       "\t CTNNA3  & intron\\_variant\\&feature\\_elongation                               & 28 & 22086810 & <DUP>\\\\\n",
       "\t         & intron\\_variant\\&non\\_coding\\_transcript\\_variant\\&feature\\_elongation & 28 & 26908422 & <DUP>\\\\\n",
       "\t ASCC1   & intron\\_variant\\&feature\\_elongation                               & 28 & 28022819 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 29 &  1199982 & <DUP>\\\\\n",
       "\t CARS1   & intron\\_variant\\&feature\\_elongation                               & 29 &  2560092 & <DUP>\\\\\n",
       "\t SHANK2  & intron\\_variant\\&feature\\_elongation                               & 29 &  3070186 & <DUP>\\\\\n",
       "\t         & upstream\\_gene\\_variant                                           & 29 &  3758853 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 29 &  7216770 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 29 & 18929786 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 29 & 20060164 & <DUP>\\\\\n",
       "\t         & upstream\\_gene\\_variant                                           & 29 & 23204937 & <DUP>\\\\\n",
       "\t PRCP    & intron\\_variant\\&feature\\_elongation                               & 29 & 38556044 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 29 & 42620542 & <DUP>\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 320 × 5\n",
       "\n",
       "| SYMBOL &lt;chr&gt; | Consequence &lt;chr&gt; | CHROM &lt;chr&gt; | POS &lt;int&gt; | ALT &lt;chr&gt; |\n",
       "|---|---|---|---|---|\n",
       "| <!----> | intergenic_variant                | 1 |   1275339 | &lt;DUP&gt; |\n",
       "| PLCL2    | intron_variant&amp;feature_elongation | 1 |   3367537 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |   4427304 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |   7152053 | &lt;DUP&gt; |\n",
       "| <!----> | intron_variant&amp;feature_elongation | 1 |  13267717 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  25477750 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  47529708 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  53236659 | &lt;DUP&gt; |\n",
       "| NAALADL2 | intron_variant&amp;feature_elongation | 1 |  64894887 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  75759547 | &lt;DUP&gt; |\n",
       "| KALRN    | intron_variant&amp;feature_elongation | 1 |  88453220 | &lt;DUP&gt; |\n",
       "| ARHGAP31 | downstream_gene_variant           | 1 |  92862060 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 108437988 | &lt;DUP&gt; |\n",
       "| IMPG2    | intron_variant&amp;feature_elongation | 1 | 111440634 | &lt;DUP&gt; |\n",
       "| CADM2    | intron_variant&amp;feature_elongation | 1 | 123408453 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 125180056 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 127337009 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 153345553 | &lt;DUP&gt; |\n",
       "| PADI2    | intron_variant&amp;feature_elongation | 2 |    896085 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 |   1619392 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 |   3886512 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 |  14553628 | &lt;DUP&gt; |\n",
       "| SERPINE2 | intron_variant&amp;feature_elongation | 2 |  24032585 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 |  38098417 | &lt;DUP&gt; |\n",
       "| ACADL    | intron_variant&amp;feature_elongation | 2 |  38164553 | &lt;DUP&gt; |\n",
       "| ADAM23   | intron_variant&amp;feature_elongation | 2 |  41389000 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 |  67430957 | &lt;DUP&gt; |\n",
       "| DPP10    | intron_variant&amp;feature_elongation | 2 |  69421935 | &lt;DUP&gt; |\n",
       "| TLK1     | intron_variant&amp;feature_elongation | 2 | 108752602 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 | 113455429 | &lt;DUP&gt; |\n",
       "| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |\n",
       "| FANK1   | intron_variant&amp;feature_elongation                               | 26 | 44066920 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 26 | 48562031 | &lt;DUP&gt; |\n",
       "| INPP5A  | intron_variant&amp;feature_elongation                               | 26 | 49863932 | &lt;DUP&gt; |\n",
       "| <!----> | downstream_gene_variant                                         | 26 | 50306469 | &lt;DUP&gt; |\n",
       "| ECHS1   | intron_variant&amp;feature_elongation                               | 26 | 50374695 | &lt;DUP&gt; |\n",
       "| <!----> | intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation | 27 |  9577172 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 27 | 11197279 | &lt;DUP&gt; |\n",
       "| PRIMPOL | intron_variant&amp;feature_elongation                               | 27 | 14197236 | &lt;DUP&gt; |\n",
       "| UNC5D   | intron_variant&amp;feature_elongation                               | 27 | 30293910 | &lt;DUP&gt; |\n",
       "| <!----> | intron_variant&amp;feature_elongation                               | 27 | 33865263 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 27 | 41976031 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 27 | 42276554 | &lt;DUP&gt; |\n",
       "| <!----> | intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation | 27 | 43037771 | &lt;DUP&gt; |\n",
       "| SIPA1L2 | intron_variant&amp;feature_elongation                               | 28 |  5544508 | &lt;DUP&gt; |\n",
       "| <!----> | upstream_gene_variant                                           | 28 |  7748550 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 28 |  7912357 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 28 |  8881602 | &lt;DUP&gt; |\n",
       "| CTNNA3  | intron_variant&amp;feature_elongation                               | 28 | 22086810 | &lt;DUP&gt; |\n",
       "| <!----> | intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation | 28 | 26908422 | &lt;DUP&gt; |\n",
       "| ASCC1   | intron_variant&amp;feature_elongation                               | 28 | 28022819 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 29 |  1199982 | &lt;DUP&gt; |\n",
       "| CARS1   | intron_variant&amp;feature_elongation                               | 29 |  2560092 | &lt;DUP&gt; |\n",
       "| SHANK2  | intron_variant&amp;feature_elongation                               | 29 |  3070186 | &lt;DUP&gt; |\n",
       "| <!----> | upstream_gene_variant                                           | 29 |  3758853 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 29 |  7216770 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 29 | 18929786 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 29 | 20060164 | &lt;DUP&gt; |\n",
       "| <!----> | upstream_gene_variant                                           | 29 | 23204937 | &lt;DUP&gt; |\n",
       "| PRCP    | intron_variant&amp;feature_elongation                               | 29 | 38556044 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 29 | 42620542 | &lt;DUP&gt; |\n",
       "\n"
      ],
      "text/plain": [
       "    SYMBOL   Consequence                                                    \n",
       "1            intergenic_variant                                             \n",
       "2   PLCL2    intron_variant&feature_elongation                              \n",
       "3            intergenic_variant                                             \n",
       "4            intergenic_variant                                             \n",
       "5            intron_variant&feature_elongation                              \n",
       "6            intergenic_variant                                             \n",
       "7            intergenic_variant                                             \n",
       "8            intergenic_variant                                             \n",
       "9   NAALADL2 intron_variant&feature_elongation                              \n",
       "10           intergenic_variant                                             \n",
       "11  KALRN    intron_variant&feature_elongation                              \n",
       "12  ARHGAP31 downstream_gene_variant                                        \n",
       "13           intergenic_variant                                             \n",
       "14  IMPG2    intron_variant&feature_elongation                              \n",
       "15  CADM2    intron_variant&feature_elongation                              \n",
       "16           intergenic_variant                                             \n",
       "17           intergenic_variant                                             \n",
       "18           intergenic_variant                                             \n",
       "19  PADI2    intron_variant&feature_elongation                              \n",
       "20           intergenic_variant                                             \n",
       "21           intergenic_variant                                             \n",
       "22           intergenic_variant                                             \n",
       "23  SERPINE2 intron_variant&feature_elongation                              \n",
       "24           intergenic_variant                                             \n",
       "25  ACADL    intron_variant&feature_elongation                              \n",
       "26  ADAM23   intron_variant&feature_elongation                              \n",
       "27           intergenic_variant                                             \n",
       "28  DPP10    intron_variant&feature_elongation                              \n",
       "29  TLK1     intron_variant&feature_elongation                              \n",
       "30           intergenic_variant                                             \n",
       "⋮   ⋮        ⋮                                                              \n",
       "291 FANK1    intron_variant&feature_elongation                              \n",
       "292          intergenic_variant                                             \n",
       "293 INPP5A   intron_variant&feature_elongation                              \n",
       "294          downstream_gene_variant                                        \n",
       "295 ECHS1    intron_variant&feature_elongation                              \n",
       "296          intron_variant&non_coding_transcript_variant&feature_elongation\n",
       "297          intergenic_variant                                             \n",
       "298 PRIMPOL  intron_variant&feature_elongation                              \n",
       "299 UNC5D    intron_variant&feature_elongation                              \n",
       "300          intron_variant&feature_elongation                              \n",
       "301          intergenic_variant                                             \n",
       "302          intergenic_variant                                             \n",
       "303          intron_variant&non_coding_transcript_variant&feature_elongation\n",
       "304 SIPA1L2  intron_variant&feature_elongation                              \n",
       "305          upstream_gene_variant                                          \n",
       "306          intergenic_variant                                             \n",
       "307          intergenic_variant                                             \n",
       "308 CTNNA3   intron_variant&feature_elongation                              \n",
       "309          intron_variant&non_coding_transcript_variant&feature_elongation\n",
       "310 ASCC1    intron_variant&feature_elongation                              \n",
       "311          intergenic_variant                                             \n",
       "312 CARS1    intron_variant&feature_elongation                              \n",
       "313 SHANK2   intron_variant&feature_elongation                              \n",
       "314          upstream_gene_variant                                          \n",
       "315          intergenic_variant                                             \n",
       "316          intergenic_variant                                             \n",
       "317          intergenic_variant                                             \n",
       "318          upstream_gene_variant                                          \n",
       "319 PRCP     intron_variant&feature_elongation                              \n",
       "320          intergenic_variant                                             \n",
       "    CHROM POS       ALT  \n",
       "1   1       1275339 <DUP>\n",
       "2   1       3367537 <DUP>\n",
       "3   1       4427304 <DUP>\n",
       "4   1       7152053 <DUP>\n",
       "5   1      13267717 <DUP>\n",
       "6   1      25477750 <DUP>\n",
       "7   1      47529708 <DUP>\n",
       "8   1      53236659 <DUP>\n",
       "9   1      64894887 <DUP>\n",
       "10  1      75759547 <DUP>\n",
       "11  1      88453220 <DUP>\n",
       "12  1      92862060 <DUP>\n",
       "13  1     108437988 <DUP>\n",
       "14  1     111440634 <DUP>\n",
       "15  1     123408453 <DUP>\n",
       "16  1     125180056 <DUP>\n",
       "17  1     127337009 <DUP>\n",
       "18  1     153345553 <DUP>\n",
       "19  2        896085 <DUP>\n",
       "20  2       1619392 <DUP>\n",
       "21  2       3886512 <DUP>\n",
       "22  2      14553628 <DUP>\n",
       "23  2      24032585 <DUP>\n",
       "24  2      38098417 <DUP>\n",
       "25  2      38164553 <DUP>\n",
       "26  2      41389000 <DUP>\n",
       "27  2      67430957 <DUP>\n",
       "28  2      69421935 <DUP>\n",
       "29  2     108752602 <DUP>\n",
       "30  2     113455429 <DUP>\n",
       "⋮   ⋮     ⋮         ⋮    \n",
       "291 26    44066920  <DUP>\n",
       "292 26    48562031  <DUP>\n",
       "293 26    49863932  <DUP>\n",
       "294 26    50306469  <DUP>\n",
       "295 26    50374695  <DUP>\n",
       "296 27     9577172  <DUP>\n",
       "297 27    11197279  <DUP>\n",
       "298 27    14197236  <DUP>\n",
       "299 27    30293910  <DUP>\n",
       "300 27    33865263  <DUP>\n",
       "301 27    41976031  <DUP>\n",
       "302 27    42276554  <DUP>\n",
       "303 27    43037771  <DUP>\n",
       "304 28     5544508  <DUP>\n",
       "305 28     7748550  <DUP>\n",
       "306 28     7912357  <DUP>\n",
       "307 28     8881602  <DUP>\n",
       "308 28    22086810  <DUP>\n",
       "309 28    26908422  <DUP>\n",
       "310 28    28022819  <DUP>\n",
       "311 29     1199982  <DUP>\n",
       "312 29     2560092  <DUP>\n",
       "313 29     3070186  <DUP>\n",
       "314 29     3758853  <DUP>\n",
       "315 29     7216770  <DUP>\n",
       "316 29    18929786  <DUP>\n",
       "317 29    20060164  <DUP>\n",
       "318 29    23204937  <DUP>\n",
       "319 29    38556044  <DUP>\n",
       "320 29    42620542  <DUP>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<caption>A data.table: 317 × 5</caption>\n",
       "<thead>\n",
       "\t<tr><th scope=col>SYMBOL</th><th scope=col>Consequence</th><th scope=col>CHROM</th><th scope=col>POS</th><th scope=col>ALT</th></tr>\n",
       "\t<tr><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;chr&gt;</th><th scope=col>&lt;int&gt;</th><th scope=col>&lt;chr&gt;</th></tr>\n",
       "</thead>\n",
       "<tbody>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td><span style=white-space:pre-wrap>   602765</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td><span style=white-space:pre-wrap>  3936817</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 14279736</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 29953460</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>CADM2   </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td> 33876430</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 47658649</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>TMEM39A </td><td><span style=white-space:pre-wrap>downstream_gene_variant          </span></td><td>1</td><td> 64208015</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>ITGB5   </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td> 69283839</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 71079825</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 81331560</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 88471586</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>NAALADL2</td><td>intron_variant&amp;feature_elongation</td><td>1</td><td> 91710880</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td> 92478629</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>109877865</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>122001281</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>131919669</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td>144139446</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>150293464</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>153808103</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>PLCL2   </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td>154031996</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>155416110</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>KCNH8   </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td>156478658</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>1</td><td>157078680</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>KAT2B   </span></td><td>intron_variant&amp;feature_elongation</td><td>1</td><td>157319928</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td><span style=white-space:pre-wrap>   221436</span></td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>downstream_gene_variant          </span></td><td>2</td><td> 18210663</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td> 41580166</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>KIF5C   </span></td><td>intron_variant&amp;feature_elongation</td><td>2</td><td> 47301693</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td> 68723736</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>        </span></td><td><span style=white-space:pre-wrap>intergenic_variant               </span></td><td>2</td><td> 98051900</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td>intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation</td><td>25</td><td>20325533</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>25</td><td>29100480</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>AUTS2  </span></td><td><span style=white-space:pre-wrap>downstream_gene_variant                                        </span></td><td>25</td><td>29771803</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>25</td><td>30926198</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>26</td><td> 3720509</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>26</td><td> 5626446</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>26</td><td> 8361857</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>SORCS3 </td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>26</td><td>25704515</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>26</td><td>27461280</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>26</td><td>49913554</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>27</td><td> 9263567</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>27</td><td> 9264901</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>27</td><td>42942224</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>27</td><td>43239137</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>SIPA1L2</td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>28</td><td> 5456189</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>28</td><td> 8087260</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>PALD1  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>28</td><td>26755278</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>PALD1  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>28</td><td>26756822</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>ASCC1  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>28</td><td>28243048</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>28</td><td>40234149</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>29</td><td> 3107977</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>PRCP   </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>29</td><td>12779092</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>upstream_gene_variant                                          </span></td><td>29</td><td>28029307</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>29</td><td>29542244</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intergenic_variant                                             </span></td><td>29</td><td>31176073</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>NFRKB  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>29</td><td>36081183</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>INCENP </td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>29</td><td>40616189</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td>SHANK2 </td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>29</td><td>48078795</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>CARS1  </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>29</td><td>48611818</td><td>&lt;DUP&gt;</td></tr>\n",
       "\t<tr><td><span style=white-space:pre-wrap>       </span></td><td><span style=white-space:pre-wrap>intron_variant&amp;feature_elongation                              </span></td><td>29</td><td>50268589</td><td>&lt;DUP&gt;</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "A data.table: 317 × 5\n",
       "\\begin{tabular}{r|lllll}\n",
       " SYMBOL & Consequence & CHROM & POS & ALT\\\\\n",
       " <chr> & <chr> & <chr> & <int> & <chr>\\\\\n",
       "\\hline\n",
       "\t          & intergenic\\_variant                & 1 &    602765 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &   3936817 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  14279736 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  29953460 & <DUP>\\\\\n",
       "\t CADM2    & intron\\_variant\\&feature\\_elongation & 1 &  33876430 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  47658649 & <DUP>\\\\\n",
       "\t TMEM39A  & downstream\\_gene\\_variant           & 1 &  64208015 & <DUP>\\\\\n",
       "\t ITGB5    & intron\\_variant\\&feature\\_elongation & 1 &  69283839 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  71079825 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  81331560 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  88471586 & <DUP>\\\\\n",
       "\t NAALADL2 & intron\\_variant\\&feature\\_elongation & 1 &  91710880 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 &  92478629 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 109877865 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 122001281 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 131919669 & <DUP>\\\\\n",
       "\t          & intron\\_variant\\&feature\\_elongation & 1 & 144139446 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 150293464 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 153808103 & <DUP>\\\\\n",
       "\t PLCL2    & intron\\_variant\\&feature\\_elongation & 1 & 154031996 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 155416110 & <DUP>\\\\\n",
       "\t KCNH8    & intron\\_variant\\&feature\\_elongation & 1 & 156478658 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 1 & 157078680 & <DUP>\\\\\n",
       "\t KAT2B    & intron\\_variant\\&feature\\_elongation & 1 & 157319928 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 &    221436 & <DUP>\\\\\n",
       "\t          & downstream\\_gene\\_variant           & 2 &  18210663 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 &  41580166 & <DUP>\\\\\n",
       "\t KIF5C    & intron\\_variant\\&feature\\_elongation & 2 &  47301693 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 &  68723736 & <DUP>\\\\\n",
       "\t          & intergenic\\_variant                & 2 &  98051900 & <DUP>\\\\\n",
       "\t ⋮ & ⋮ & ⋮ & ⋮ & ⋮\\\\\n",
       "\t         & intron\\_variant\\&non\\_coding\\_transcript\\_variant\\&feature\\_elongation & 25 & 20325533 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 25 & 29100480 & <DUP>\\\\\n",
       "\t AUTS2   & downstream\\_gene\\_variant                                         & 25 & 29771803 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 25 & 30926198 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 26 &  3720509 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 26 &  5626446 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 26 &  8361857 & <DUP>\\\\\n",
       "\t SORCS3  & intron\\_variant\\&feature\\_elongation                               & 26 & 25704515 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 26 & 27461280 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 26 & 49913554 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 27 &  9263567 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 27 &  9264901 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 27 & 42942224 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 27 & 43239137 & <DUP>\\\\\n",
       "\t SIPA1L2 & intron\\_variant\\&feature\\_elongation                               & 28 &  5456189 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 28 &  8087260 & <DUP>\\\\\n",
       "\t PALD1   & intron\\_variant\\&feature\\_elongation                               & 28 & 26755278 & <DUP>\\\\\n",
       "\t PALD1   & intron\\_variant\\&feature\\_elongation                               & 28 & 26756822 & <DUP>\\\\\n",
       "\t ASCC1   & intron\\_variant\\&feature\\_elongation                               & 28 & 28243048 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 28 & 40234149 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 29 &  3107977 & <DUP>\\\\\n",
       "\t PRCP    & intron\\_variant\\&feature\\_elongation                               & 29 & 12779092 & <DUP>\\\\\n",
       "\t         & upstream\\_gene\\_variant                                           & 29 & 28029307 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 29 & 29542244 & <DUP>\\\\\n",
       "\t         & intergenic\\_variant                                              & 29 & 31176073 & <DUP>\\\\\n",
       "\t NFRKB   & intron\\_variant\\&feature\\_elongation                               & 29 & 36081183 & <DUP>\\\\\n",
       "\t INCENP  & intron\\_variant\\&feature\\_elongation                               & 29 & 40616189 & <DUP>\\\\\n",
       "\t SHANK2  & intron\\_variant\\&feature\\_elongation                               & 29 & 48078795 & <DUP>\\\\\n",
       "\t CARS1   & intron\\_variant\\&feature\\_elongation                               & 29 & 48611818 & <DUP>\\\\\n",
       "\t         & intron\\_variant\\&feature\\_elongation                               & 29 & 50268589 & <DUP>\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "A data.table: 317 × 5\n",
       "\n",
       "| SYMBOL &lt;chr&gt; | Consequence &lt;chr&gt; | CHROM &lt;chr&gt; | POS &lt;int&gt; | ALT &lt;chr&gt; |\n",
       "|---|---|---|---|---|\n",
       "| <!----> | intergenic_variant                | 1 |    602765 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |   3936817 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  14279736 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  29953460 | &lt;DUP&gt; |\n",
       "| CADM2    | intron_variant&amp;feature_elongation | 1 |  33876430 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  47658649 | &lt;DUP&gt; |\n",
       "| TMEM39A  | downstream_gene_variant           | 1 |  64208015 | &lt;DUP&gt; |\n",
       "| ITGB5    | intron_variant&amp;feature_elongation | 1 |  69283839 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  71079825 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  81331560 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  88471586 | &lt;DUP&gt; |\n",
       "| NAALADL2 | intron_variant&amp;feature_elongation | 1 |  91710880 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 |  92478629 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 109877865 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 122001281 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 131919669 | &lt;DUP&gt; |\n",
       "| <!----> | intron_variant&amp;feature_elongation | 1 | 144139446 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 150293464 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 153808103 | &lt;DUP&gt; |\n",
       "| PLCL2    | intron_variant&amp;feature_elongation | 1 | 154031996 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 155416110 | &lt;DUP&gt; |\n",
       "| KCNH8    | intron_variant&amp;feature_elongation | 1 | 156478658 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 1 | 157078680 | &lt;DUP&gt; |\n",
       "| KAT2B    | intron_variant&amp;feature_elongation | 1 | 157319928 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 |    221436 | &lt;DUP&gt; |\n",
       "| <!----> | downstream_gene_variant           | 2 |  18210663 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 |  41580166 | &lt;DUP&gt; |\n",
       "| KIF5C    | intron_variant&amp;feature_elongation | 2 |  47301693 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 |  68723736 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                | 2 |  98051900 | &lt;DUP&gt; |\n",
       "| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |\n",
       "| <!----> | intron_variant&amp;non_coding_transcript_variant&amp;feature_elongation | 25 | 20325533 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 25 | 29100480 | &lt;DUP&gt; |\n",
       "| AUTS2   | downstream_gene_variant                                         | 25 | 29771803 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 25 | 30926198 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 26 |  3720509 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 26 |  5626446 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 26 |  8361857 | &lt;DUP&gt; |\n",
       "| SORCS3  | intron_variant&amp;feature_elongation                               | 26 | 25704515 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 26 | 27461280 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 26 | 49913554 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 27 |  9263567 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 27 |  9264901 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 27 | 42942224 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 27 | 43239137 | &lt;DUP&gt; |\n",
       "| SIPA1L2 | intron_variant&amp;feature_elongation                               | 28 |  5456189 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 28 |  8087260 | &lt;DUP&gt; |\n",
       "| PALD1   | intron_variant&amp;feature_elongation                               | 28 | 26755278 | &lt;DUP&gt; |\n",
       "| PALD1   | intron_variant&amp;feature_elongation                               | 28 | 26756822 | &lt;DUP&gt; |\n",
       "| ASCC1   | intron_variant&amp;feature_elongation                               | 28 | 28243048 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 28 | 40234149 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 29 |  3107977 | &lt;DUP&gt; |\n",
       "| PRCP    | intron_variant&amp;feature_elongation                               | 29 | 12779092 | &lt;DUP&gt; |\n",
       "| <!----> | upstream_gene_variant                                           | 29 | 28029307 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 29 | 29542244 | &lt;DUP&gt; |\n",
       "| <!----> | intergenic_variant                                              | 29 | 31176073 | &lt;DUP&gt; |\n",
       "| NFRKB   | intron_variant&amp;feature_elongation                               | 29 | 36081183 | &lt;DUP&gt; |\n",
       "| INCENP  | intron_variant&amp;feature_elongation                               | 29 | 40616189 | &lt;DUP&gt; |\n",
       "| SHANK2  | intron_variant&amp;feature_elongation                               | 29 | 48078795 | &lt;DUP&gt; |\n",
       "| CARS1   | intron_variant&amp;feature_elongation                               | 29 | 48611818 | &lt;DUP&gt; |\n",
       "| <!----> | intron_variant&amp;feature_elongation                               | 29 | 50268589 | &lt;DUP&gt; |\n",
       "\n"
      ],
      "text/plain": [
       "    SYMBOL   Consequence                                                    \n",
       "1            intergenic_variant                                             \n",
       "2            intergenic_variant                                             \n",
       "3            intergenic_variant                                             \n",
       "4            intergenic_variant                                             \n",
       "5   CADM2    intron_variant&feature_elongation                              \n",
       "6            intergenic_variant                                             \n",
       "7   TMEM39A  downstream_gene_variant                                        \n",
       "8   ITGB5    intron_variant&feature_elongation                              \n",
       "9            intergenic_variant                                             \n",
       "10           intergenic_variant                                             \n",
       "11           intergenic_variant                                             \n",
       "12  NAALADL2 intron_variant&feature_elongation                              \n",
       "13           intergenic_variant                                             \n",
       "14           intergenic_variant                                             \n",
       "15           intergenic_variant                                             \n",
       "16           intergenic_variant                                             \n",
       "17           intron_variant&feature_elongation                              \n",
       "18           intergenic_variant                                             \n",
       "19           intergenic_variant                                             \n",
       "20  PLCL2    intron_variant&feature_elongation                              \n",
       "21           intergenic_variant                                             \n",
       "22  KCNH8    intron_variant&feature_elongation                              \n",
       "23           intergenic_variant                                             \n",
       "24  KAT2B    intron_variant&feature_elongation                              \n",
       "25           intergenic_variant                                             \n",
       "26           downstream_gene_variant                                        \n",
       "27           intergenic_variant                                             \n",
       "28  KIF5C    intron_variant&feature_elongation                              \n",
       "29           intergenic_variant                                             \n",
       "30           intergenic_variant                                             \n",
       "⋮   ⋮        ⋮                                                              \n",
       "288          intron_variant&non_coding_transcript_variant&feature_elongation\n",
       "289          intergenic_variant                                             \n",
       "290 AUTS2    downstream_gene_variant                                        \n",
       "291          intergenic_variant                                             \n",
       "292          intergenic_variant                                             \n",
       "293          intergenic_variant                                             \n",
       "294          intergenic_variant                                             \n",
       "295 SORCS3   intron_variant&feature_elongation                              \n",
       "296          intergenic_variant                                             \n",
       "297          intergenic_variant                                             \n",
       "298          intergenic_variant                                             \n",
       "299          intergenic_variant                                             \n",
       "300          intergenic_variant                                             \n",
       "301          intergenic_variant                                             \n",
       "302 SIPA1L2  intron_variant&feature_elongation                              \n",
       "303          intergenic_variant                                             \n",
       "304 PALD1    intron_variant&feature_elongation                              \n",
       "305 PALD1    intron_variant&feature_elongation                              \n",
       "306 ASCC1    intron_variant&feature_elongation                              \n",
       "307          intergenic_variant                                             \n",
       "308          intergenic_variant                                             \n",
       "309 PRCP     intron_variant&feature_elongation                              \n",
       "310          upstream_gene_variant                                          \n",
       "311          intergenic_variant                                             \n",
       "312          intergenic_variant                                             \n",
       "313 NFRKB    intron_variant&feature_elongation                              \n",
       "314 INCENP   intron_variant&feature_elongation                              \n",
       "315 SHANK2   intron_variant&feature_elongation                              \n",
       "316 CARS1    intron_variant&feature_elongation                              \n",
       "317          intron_variant&feature_elongation                              \n",
       "    CHROM POS       ALT  \n",
       "1   1        602765 <DUP>\n",
       "2   1       3936817 <DUP>\n",
       "3   1      14279736 <DUP>\n",
       "4   1      29953460 <DUP>\n",
       "5   1      33876430 <DUP>\n",
       "6   1      47658649 <DUP>\n",
       "7   1      64208015 <DUP>\n",
       "8   1      69283839 <DUP>\n",
       "9   1      71079825 <DUP>\n",
       "10  1      81331560 <DUP>\n",
       "11  1      88471586 <DUP>\n",
       "12  1      91710880 <DUP>\n",
       "13  1      92478629 <DUP>\n",
       "14  1     109877865 <DUP>\n",
       "15  1     122001281 <DUP>\n",
       "16  1     131919669 <DUP>\n",
       "17  1     144139446 <DUP>\n",
       "18  1     150293464 <DUP>\n",
       "19  1     153808103 <DUP>\n",
       "20  1     154031996 <DUP>\n",
       "21  1     155416110 <DUP>\n",
       "22  1     156478658 <DUP>\n",
       "23  1     157078680 <DUP>\n",
       "24  1     157319928 <DUP>\n",
       "25  2        221436 <DUP>\n",
       "26  2      18210663 <DUP>\n",
       "27  2      41580166 <DUP>\n",
       "28  2      47301693 <DUP>\n",
       "29  2      68723736 <DUP>\n",
       "30  2      98051900 <DUP>\n",
       "⋮   ⋮     ⋮         ⋮    \n",
       "288 25    20325533  <DUP>\n",
       "289 25    29100480  <DUP>\n",
       "290 25    29771803  <DUP>\n",
       "291 25    30926198  <DUP>\n",
       "292 26     3720509  <DUP>\n",
       "293 26     5626446  <DUP>\n",
       "294 26     8361857  <DUP>\n",
       "295 26    25704515  <DUP>\n",
       "296 26    27461280  <DUP>\n",
       "297 26    49913554  <DUP>\n",
       "298 27     9263567  <DUP>\n",
       "299 27     9264901  <DUP>\n",
       "300 27    42942224  <DUP>\n",
       "301 27    43239137  <DUP>\n",
       "302 28     5456189  <DUP>\n",
       "303 28     8087260  <DUP>\n",
       "304 28    26755278  <DUP>\n",
       "305 28    26756822  <DUP>\n",
       "306 28    28243048  <DUP>\n",
       "307 28    40234149  <DUP>\n",
       "308 29     3107977  <DUP>\n",
       "309 29    12779092  <DUP>\n",
       "310 29    28029307  <DUP>\n",
       "311 29    29542244  <DUP>\n",
       "312 29    31176073  <DUP>\n",
       "313 29    36081183  <DUP>\n",
       "314 29    40616189  <DUP>\n",
       "315 29    48078795  <DUP>\n",
       "316 29    48611818  <DUP>\n",
       "317 29    50268589  <DUP>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "auto_angus[SVTYPE=='DUP',c('SYMBOL','Consequence','CHROM','POS','ALT')]\n",
    "auto_UCD[SVTYPE=='DUP',c('SYMBOL','Consequence','CHROM','POS','ALT')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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   "file_extension": ".r",
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