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Plant-Food-Research-Open · Nov 5, 2024 · 6e27250 · 6e27250
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diff --git a/hic/FI1.hic b/hic/FI1.hic
diff --git a/hic/hicqc/SRR8238190.on.FI1_qc_report.pdf b/hic/hicqc/SRR8238190.on.FI1_qc_report.pdf
diff --git a/index.html b/index.html
diff --git a/kraken2/FI1.kraken2.krona.html b/kraken2/FI1.kraken2.krona.html
diff --git a/ncbi_fcs_gx/FI1.fcs.gx.krona.html b/ncbi_fcs_gx/FI1.fcs.gx.krona.html
@@ -6628,98 +6628,98 @@
  <count><val>8</val></count>
  <magnitude><val>35023690</val></magnitude>
  <node name="Eukaryota">
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   <rank><val>superkingdom</val></rank>
   <magnitude><val>35023690</val></magnitude>
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   <count><val>8</val></count>
   <taxon><val href="2759">2759</val></taxon>
   <node name="Opisthokonta">
-   <count><val>8</val></count>
    <score><val>11695.7</val></score>
    <taxon><val href="33154">33154</val></taxon>
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    <rank><val>clade</val></rank>
    <magnitude><val>35023690</val></magnitude>
    <node name="Fungi">
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     <score><val>11695.7</val></score>
-    <taxon><val href="4751">4751</val></taxon>
-    <rank><val>kingdom</val></rank>
     <magnitude><val>35023690</val></magnitude>
+    <rank><val>kingdom</val></rank>
+    <count><val>8</val></count>
+    <taxon><val href="4751">4751</val></taxon>
     <node name="Dikarya">
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      <magnitude><val>35023690</val></magnitude>
      <rank><val>subkingdom</val></rank>
-     <taxon><val href="451864">451864</val></taxon>
-     <score><val>11695.7</val></score>
      <count><val>8</val></count>
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      <node name="Ascomycota">
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-      <score><val>11695.7</val></score>
       <count><val>8</val></count>
-      <magnitude><val>35023690</val></magnitude>
+      <taxon><val href="4890">4890</val></taxon>
       <rank><val>phylum</val></rank>
+      <magnitude><val>35023690</val></magnitude>
+      <score><val>11695.7</val></score>
       <node name="saccharomyceta">
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        <score><val>11695.7</val></score>
+       <count><val>8</val></count>
        <taxon><val href="716545">716545</val></taxon>
-       <rank><val>clade</val></rank>
        <magnitude><val>35023690</val></magnitude>
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        <node name="Pezizomycotina">
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         <score><val>11695.7</val></score>
-        <count><val>8</val></count>
-        <magnitude><val>35023690</val></magnitude>
         <rank><val>subphylum</val></rank>
+        <magnitude><val>35023690</val></magnitude>
+        <taxon><val href="147538">147538</val></taxon>
+        <count><val>8</val></count>
         <node name="leotiomyceta">
+         <score><val>11695.7</val></score>
          <taxon><val href="716546">716546</val></taxon>
          <count><val>8</val></count>
-         <score><val>11695.7</val></score>
-         <magnitude><val>35023690</val></magnitude>
          <rank><val>clade</val></rank>
+         <magnitude><val>35023690</val></magnitude>
          <node name="sordariomyceta">
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-          <rank><val>clade</val></rank>
           <taxon><val href="715989">715989</val></taxon>
-          <score><val>11695.7</val></score>
           <count><val>8</val></count>
+          <rank><val>clade</val></rank>
+          <magnitude><val>35023690</val></magnitude>
+          <score><val>11695.7</val></score>
           <node name="Sordariomycetes">
-           <rank><val>class</val></rank>
-           <magnitude><val>35023690</val></magnitude>
-           <count><val>8</val></count>
            <score><val>11695.7</val></score>
+           <count><val>8</val></count>
            <taxon><val href="147550">147550</val></taxon>
+           <magnitude><val>35023690</val></magnitude>
+           <rank><val>class</val></rank>
            <node name="Hypocreomycetidae">
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-            <rank><val>subclass</val></rank>
-            <taxon><val href="222543">222543</val></taxon>
             <count><val>8</val></count>
+            <taxon><val href="222543">222543</val></taxon>
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             <score><val>11695.7</val></score>
             <node name="Hypocreales">
              <taxon><val href="5125">5125</val></taxon>
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              <count><val>8</val></count>
              <magnitude><val>35023690</val></magnitude>
              <rank><val>order</val></rank>
+             <score><val>11695.7</val></score>
              <node name="Clavicipitaceae">
+              <score><val>11695.7</val></score>
               <rank><val>family</val></rank>
               <magnitude><val>35023690</val></magnitude>
-              <count><val>8</val></count>
-              <score><val>11695.7</val></score>
               <taxon><val href="34397">34397</val></taxon>
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               <node name="Epichloe">
                <magnitude><val>35023690</val></magnitude>
                <rank><val>genus</val></rank>
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                <taxon><val href="5112">5112</val></taxon>
                <score><val>11695.7</val></score>
-               <count><val>8</val></count>
                <node name="Epichloe bromicola">
-                <taxon><val href="79588">79588</val></taxon>
                 <score><val>11695.7</val></score>
                 <count><val>8</val></count>
-                <magnitude><val>35023690</val></magnitude>
-                <rank><val>species</val></rank>
                 <members>
                  <vals><val>CP031385.1</val><val>CP031386.1</val><val>CP031387.1</val><val>CP031388.1</val><val>CP031389.1</val><val>CP031390.1</val><val>CP031391.1</val><val>CP031392.1</val></vals>
                 </members>
+                <taxon><val href="79588">79588</val></taxon>
+                <magnitude><val>35023690</val></magnitude>
+                <rank><val>species</val></rank>
                </node>
               </node>
              </node>

diff --git a/synteny/FI1.on.JAD.all/FI1.on.JAD.all.html b/synteny/FI1.on.JAD.all/FI1.on.JAD.all.html
diff --git a/synteny/FI1.on.TT_2021a.all/FI1.on.TT_2021a.all.html b/synteny/FI1.on.TT_2021a.all/FI1.on.TT_2021a.all.html