The final average BRLMM call rate across the entire sample reached the high level of 99.14%. However, out of the initial full-set of 500,568 SNPs, we discarded 32,961 SNPs with sample call rates < 95%, another 36,965 SNPs with allele frequencies deviating from Hardy-Weinberg equilibrium (HWE) (P < 0.001) and 51,323 SNPs with minor allele frequencies (MAF) < 1%. Therefore, the final SNP set maintained in the subsequent analyses contained 379,319 SNPs, yielding an average marker spacing of ∼7.9 kb throughout the human genome.
