We compared heterozygosity patterns by measuring the differences in average heterozygosity between Europeans and East Asians. We measured these differences between the two ancestry groups in a 600-SNP region around each SNP under study. We used sliding windows of 50 consecutive SNPs, with a step of 5 SNPs. As predicted, windows immediately centered on non-replicated SNPs presented significantly larger differences in average heterozygosity across populations than windows centered on replicated SNPs (0.048 vs. 0.019, P<0.009, Figure 2).
