Fig. 5: Population results in CYP21A2, PMS2 and OPN1LW/OPN1MW.

a Paraphase resolved haplotypes in the RCCX module, realigned to the RCCX copy that encodes CYP21A2. Haplotypes of the same color (purple or green) are from the same allele. Longer haplotypes represent the last RCCX copies in the array on each allele, and shorter haplotypes represent remaining copies. Two examples are shown, including a sample with no CNV (top) and a sample with RCCX duplication (bottom), which carries an allele (purple) with a wild-type copy of CYP21A2 and another copy of CYP21A2 harboring a pathogenic variant Q319X (red arrow). b Frequency of the total RCCX CN per allele across populations. c Paraphase resolved haplotypes in PMS2/PMS2CL, realigned to PMS2. Exon numbers are labeled with respect to PMS2. Three examples are shown, including a sample with no gene conversion and two samples carrying alleles converted in Exon 12 or Exons 13-14 (conversions in PMS2 shown in black boxes and conversions in PMS2CL shown in red boxes). d Frequency of gene conversions between PMS2 and PMS2CL across populations in Exon 12 and Exons 13-14. e Paraphase resolved haplotypes in OPN1LW/OPN1MW, realigned to OPN1LW. Longer haplotypes represent the first copies of the repeat in the array on each allele, and shorter haplotypes represent remaining copies. The first two copies of the repeat on each allele are colored in green, and the blue color indicates gene copies beyond the second copy in the array, i.e. not expressed. OPN1LW and OPN1MW are assigned based on variants in Exon 5 (red arrows). Two examples are shown, including a normal allele with a copy of OPN1LW followed by a copy of OPN1MW (top) and an allele (deutan) with a copy of OPN1LW followed by a copy of OPN1LW (bottom, the third unexpressed copy marked in blue). f Distribution of the summed CN of OPN1LW and OPN1MW per allele across populations.