The mean number of SNVs per exome (homozygous nonreference and heterozygous genotypes) was 13,595, and ∼66% (8893) of these sites were heterozygous. As expected, AAs had significantly more SNVs per exome than EAs (15,073 versus 12,406, Mann-Whitney test, P < 10−16), which is true for all classes of sites (Fig. 4B). Moreover, on average, each individual possessed 35 nonsense variants and was homozygous for at least one nonreference nonsense variant; 318 individuals (181 AAs and 137 EAs) were compound heterozygotes for nonsense SNVs. The mean number of novel SNVs per individual was 549 overall, but AAs had more than twice the number of novel SNVs compared with EAs (762 versus 362, respectively; P= 1.9 × 10−7 correcting for differences in the mean number of SNVs between populations). The fraction of overall variation that was novel in AAs was higher than in EAs (5 and 3%, respectively; P < 10−16). Lastly, although most protein-coding variants were rare in the full AA and EA population samples, the majority of SNVs found in an average individual were common (Fig. 4C).
