Supplemental Material for Brandt et al., 2018

Extended Materials and Methods shows the modification of VCFtools source code to get variance components of Fst. File S1 shows the constraints of minor allele frequency on Fst. File S2 is a detailed description of the balancing selection simulations. Figure S4 shows Fst as a function of MAF for each HLA gene. Figure S5 is a flowchart describing the steps of the resampling algorithm used to account for LD among HLA SNPs. Figure S6 shows distributions of Fst in bins of MAF lower than 0.01. Figure S7 shows distributions of Fst per MAF bin, including outliers. Figure S8 shows hierarchical population differentiation (Fct and Fsc) along chromosome 6. Table S1 shows sample sizes per population. Table S2 is a list of peri-HLA genes and their genomic coordinates. Table S3 is a list of sites excluded due to excess of genotyping errors. Table S4 shows the results of the statistical test of differences in Fst distributions in HLA and non-HLA SNPs, accounting for LD.