Extended Data Fig. 10: Number of variants called from 1KGP and SGDP individuals.

a. More variants are called on the X-PARs when using the sex chromosome complement reference approach (calling variants in diploid mode on PARs) than the non-masked approach (calling variants in haploid mode on PARs). The 1KGP results for GRCh38-Y are from Aganezov et al.⁶⁶, which was performed on CHM13v1.0+GRCh38-Y. b. Num. of variants called from each 1KGP XY sample on chromosome GRCh38-Y and T2T-Y c. Num. of variants called in the syntenic region between the two Ys. A large num. of additional variants are called on each sample attributed to the newly added, non-syntenic sequences on T2T-Y. Within the syntenic regions, a reduction in the number of variants is observed for each population except for samples from R1 haplogroups as shown in Fig. 6c. d. Aggregated total number of variants for the 279 SGDP samples per chromosome. e. SGDP genome-wide counts of variants per-sample (n = 279) demonstrate increased variation in African samples regardless of reference. Each bar in the box plot represents the 1st, 2nd (median), and 3rd quartile of the number of variants in each population. Whiskers are bound to the 1.5 × interquartile range. Data outside of the whisker ranges are shown as dots. For the SGDP samples, variants were called using T2T-CHM13+Y or GRCh38 as the reference. All variants shown in this figure were filtered for “high quality (PASS)”.