To identify the allele ΔF for common variants in the ancestry groups, we used the method proposed by Hofer and colleagues [14]. We chose this metric based on allele ΔF rather than others commonly used in population genetics (e.g., Wright’s fixation index) in order to make our analysis clear also to nonexperts in the field. For each allele i, we computed the average allele frequency pij within each ancestry group j, as well as the difference with the average frequency computed over all other populations as ΔF = |pij − p−ij|, where p−ij is the average frequency of allele i in all populations not belonging to the ancestry group j. A permutation test (n = 10,000) was performed to determine whether the MAF between the populations within ancestry groups and the rest of the populations was significantly different than expected by the chance.
