Similarly, extended stretches of homozygosity are indicative of recent inbreeding within populations28,29. Although short runs of homozygosity are commonplace, covering up to one-third of the genome and showing population differences reflective of ancient linkage disequilibrium patterns (Table 5 and Fig. 3b), very long homozygous runs exist that are clearly distinct from this process. Including two JPT individuals who have unusually high levels of homozygosity (NA18987 and NA18992) and one CEU individual (NA12874), we identified 79 homozygous regions over 3 Mb in 51 individuals, with many segments extending over 10 Mb (Supplementary Tables 7 and 8). Segments intersecting with suspected deletions were first removed from the analysis (Supplementary Text 6).
