Fig. 2.

(A) Genome-wide histogram of the number of uniquely shared sites where the Denisovan allele is at less than 1% frequency in Africans (AFR, excluding admixed African-Americans) and at more than 20% frequency in Eurasians (EUR + SAS + EAS). The counts were computed in non-overlapping 40 kb regions of the genome. The y-axis is truncated, as the vast majority of regions have zero uniquely shared sites. TBX15 and WARS2 are among the few regions that have three and four uniquely shared sites, respectively. (B) In each of the same 40 kb windows, we also computed the 95% quantile of Eurasian derived allele frequencies of all SNPs that are homozygous derived in Denisova and less than 1% derived in Africans. The figure shows a histogram of this score for all windows. The 95% quantile scores for TBX15 and WARS2 are 0.27 and 0.26, respectively.