As expected, and consistent with purifying selection, putative functional variants had an allele frequency spectrum depleted at higher allele frequencies, with putative LOF variants showing this effect more strongly (Supplementary Fig. 13). Of the low coverage nonsynonymous, stop-introducing, splice-disrupting and HGMD-DM variants, 67.3%, 77.3%, 82.2% and 84.7%, were private to single populations, compared to 61.1% for synonymous variants. Across these same functional classes, 15.8%, 25.9%, 21.6% and 19.9% of variants were found in only a single individual, compared to 11.8% of synonymous variants.
