Since population stratification can be used as a signature to detect adaptive selection, we additionally identified SVs varying in VAF amongst different populations. For each SV site we calculated a VST statistic, a measure highly correlated with FST (the fixation index)29 that can be applied to assess population stratification of biallelic and multi-allelic SVs29. We observed 1,434 highly stratified SVs (>0.2 VST, corresponding to 2.9 standard deviations (s.d.) from the mean; Supplementary Table 5), among which 578 intersected gene coding sequences (CDSs). Among these were several SVs associated with regions previously reported to be under positive selection, such as KANSL1 mCNVs (Extended Data Fig. 6) that tag a European-enriched inversion polymorphism associated with increased fecundity30. Most of the population-stratified sites, however, have not been previously described and are, thus, potential targets for future investigation of SVs undergoing adaptive selection or genetic drift. These include, for example, a 14.5 kbp intronic duplication of HERC2 enriched in East Asians (VST = 0.62 EAS-EUR).
