At least part of region is annotated as alpha satellite sequence
Region of high AT content
short error in base, low quality consensus
Region contains reads with high level of clipping
Correction applied in next assembly version
A correction for this issue will be applied in the next release
Issues discovered by primary alignments of reads to assembly
Correction deferred until next assembly release
These issues are duplicates of other issues
Based on a variant called from Element alignments
Assembly contains kmers not present in the (hybrid) set of reads
Not likely to be an assembly error
Intersects flagger calls from both HiFi and ONT reads
Region of high GA/TC content
Region of high GC content
Child has 0/1 genotype w.r.t. this haplotype
Child has 1/2 genotype w.r.t. this haplotype
Extra attention is needed
This issue has evidence in the HiFi reads
Region with higher than expected HiFi coverage (possible collapse)
Region with higher than expected ONT coverage (possible collapse)
At least part of region is annotated HSat2
At least part of region is annotated HSat3
This issue describes a poor quality or misassembled region in the assembly
Issue discovered from homozygous non-reference DeepVariant calls on long read data
False homozygosity in assembly discovered by DeepVariant hom non ref call on aligns to both haps