For RVs, we analyzed the occurrences of functional RVs among all of the ancestry groups and used an equation to estimate ancestry differences in the occurrence of functional RVs. Using VARIANT annotation analysis, we distinguished functional variants from nonfunctional variants. Based on this information, for each gene we estimated the occurrence of functional RVs as the ratio of functional RVs to all observed variants. Specifically, for each gene i, we computed the average ratio rij within each ancestry group j, as well as the difference with the average ratio computed over all other populations as rΔF = |rij − r−ij|, where r−ij is the average ratio of gene i in all populations not belonging to the ancestry group j. A permutation test (n = 10,000) was performed to evaluate the significance of differences between the populations within an ancestry group compared with the rest of the populations.
