duos; (5) variants with a Hardy–Weinberg P < 1 × 10−4; (6) SNPs with sex difference in allele frequency ≥ 0.2 for autosomes or XY; (7) SNPs with sex difference in heterozygosity > 0.3 for autosomes or XY; and (8) positional duplicates. Sites were further restricted to chromosomes 1–22, X or XY, and only variants with available strand information were included. After SNP quality control, a total of 1,402,653 MEGA variants remained for further analyses (for further details see Supplementary Information 3).
