To apply our SNP selection method, first a set of 179 SNPs found in both our re-sequencing SNP set and in HapMap was identified, and 120 tagSNPs were picked to represent them with MAF ≥2% and r2 = 1.0 in the re-sequencing set. These SNPs were then prioritized in the selection of additional tagSNPs to represent the set of HapMap SNPs in the region that had minimum MAF = 5%, at r2 = 0.8. They were also prioritized in the selection of additional tagSNPs to represent the other re-sequencing SNPs, with MAF ≥2%, at r2 = 1.0.
