Fig. 3

Region 148. IGV screenshots [50] are shown with variant calls for in-house sample P. a The presence of numerous ASDP-associated variants as well as a structural variant associated with the alternate locus KI270808.1 clearly suggest that the sample is homozygous for the KI270808.1 rather than for the REF-HAP sequence for region 148. Note that most of the variants that correspond to ASDPs are homozygous, suggesting that KI270808.1 is present in the homozygous state. An additional non-ASDP variant is present. Variants corresponding to 50 of the 52 ASDPs shown are listed in dbSNP. b The corresponding region on the alternate locus KI270808.1 was alignable well. Only the single non-ASDP-associated variant is called. IGV shows supplemental reads in blue (i.e., reads that map to the primary assembly as well as to an alternate locus). ASDP alignable scaffold-discrepant position, SNV single nucleotide variant, SV structural variant, IGV Integrative Genomics Viewer