We explored the population genetic properties of SVs among five continental groups—Africa (AFR), the Americas (AMR), East Asia (EAS), Europe (EUR) and South Asia (SAS). The bulk of SVs occur at low frequency (65% exhibit VAF < 0.2%) consistent amongst individual SV classes (Extended Data Figs 2, 3). While rare SVs are typically specific to individual continental groups, at VAF ≥ 2% nearly all SVs are shared across continents (Fig. 1d, Extended Data Fig. 3). Notably, we identified 1,075 SVs with VAF > 50% (889 biallelic deletions, 2 biallelic duplications, 90 mCNVs, 88 MEIs and 6 inversions) encompassing 5 Mbp, sites of interest for future updates to the human reference genome. We estimated the mutation rate for each SV class using Waterson’s estimator of θ, for example, ascertaining a mutation rate of 0.113 deletions per haploid genome generation, a threefold higher estimate compared with previous reports10,24, probably owing to our increased power for detecting variants < 5 kbp (Supplementary Note).
