Labels

• alpha_sat

  At least part of region is annotated as alpha satellite sequence
• at

  Region of high AT content
• base_error

  short error in base, low quality consensus
• clipped

  Region contains reads with high level of clipping
• correction_applied

  Correction applied in next assembly version
• correction_pending

  A correction for this issue will be applied in the next release
• coverage_pri

  Issues discovered by primary alignments of reads to assembly
• deferred

  Correction deferred until next assembly release
• duplicate

  These issues are duplicates of other issues
• element_evidence

  Based on a variant called from Element alignments
• error_kmer

  Assembly contains kmers not present in the (hybrid) set of reads
• false_positive

  Not likely to be an assembly error
• flagger_intersect

  Intersects flagger calls from both HiFi and ONT reads
• ga_tc

  Region of high GA/TC content
• gc

  Region of high GC content
• geno_01

  Child has 0/1 genotype w.r.t. this haplotype
• geno_02
• geno_12

  Child has 1/2 genotype w.r.t. this haplotype
• haplotype_switch

  haplotype switch
• help_wanted

  Extra attention is needed
• hifi_evidence

  This issue has evidence in the HiFi reads
• high_cov_hifi

  Region with higher than expected HiFi coverage (possible collapse)
• high_cov_ont

  Region with higher than expected ONT coverage (possible collapse)
• homopolymer
• hsat2

  At least part of region is annotated HSat2
• hsat3

  At least part of region is annotated HSat3
• invalid

  This doesn't seem right
• large_error

  This issue describes a poor quality or misassembled region in the assembly
• longread_homnonref

  Issue discovered from homozygous non-reference DeepVariant calls on long read data
• longread_missinghet

  False homozygosity in assembly discovered by DeepVariant hom non ref call on aligns to both haps