Extended Data Fig. 2: Additional CNV genotyping at key loci.
From: Protein-altering variants at copy number-variable regions influence diverse human phenotypes
a, Schematic of discordant WGS reads that confirm tandem duplications and indicate breakpoint locations. b, We genotyped the CCNF exon 3 IED using discordant WGS reads (shown for a carrier in UKB) to assess precision and recall of WES-based calls from our HMM. c, IGV tracks of WES and WGS alignments for an RGL3 deletion carrier. Top, WES features used in optimized breakpoint-based genotyping; bottom, independent confirmation of deletion from WGS. d,e, In All of Us (AoU), chimeric WGS reads and within-deletion read counts allowed the RGL3 and CTRB2 deletions to be cleanly genotyped. (The homozygous deletion cluster for RGL3 contained <20 carriers, so to comply with AoU policy, the Hom-DEL line depicted is predicted from the heterozygous cluster).
