Considering only fully resolved events with genotyping rates above 95% (n = 541), we identified between 232 kb and 418 kb of retained ancestral sequence per diploid individual. Allele frequencies of assembled retained sequences are greater than those observed for SNVs and indels, with 76.7% of the assembled sequences present at allele frequency of more than 5% and only 12% of assembled sequences with allele frequency of less than 0.5% (Supplementary Fig. 23). This could reflect difficulty in assembling rare haplotypes. Consistent with observations for SNVs and indels, individuals of African ancestry had, on average, more non-reference alleles (Fig. 3b, Supplementary Fig. 24 and Supplementary Table 11). The overwhelming majority of assembled events are shared by multiple continental groups. We found 58 genic (5 of which are exonic) and 48 intergenic sequences present in a homozygous state in all individuals in the cohort, suggesting that the reference sequence may be incomplete at particular loci, directly affecting the annotation of common forms of genes, such as UBE2QL1, FOXO6 and FURIN (Supplementary Fig. 25).
