The overall allele frequency spectrum of CNPs resembled that of the SNPs ascertained by resequencing: most variants were at low frequency (Fig. 1b), but most heterozygosity was due to a limited set of common variants. This extends an observation previously made in the original HapMap population samples7 to additional populations. The allele frequency spectrum of common CNPs (MAF >10%) was similar across populations, but differed markedly at lower frequencies. African-ancestry and admixed populations showed by far the greatest number of variants with MAF <5%, and had a higher average number of CNPs differing in copy number between two individuals (160–171) than non-admixed populations without African ancestry (127–142) (Fig. 1b).
