Table 1.

Number of SNPs before and after pruning.

Criteria	Number
Total no. of SNPs before pruning	569,244
Failed HWE test	173,955
Failed missingness test	1,934
Failed SNP frequency test	61,167
Mendelian errors detected	349
Remaining SNPs after pruninga	341,191

^aRemaining SNPs refer to those without deviations from Hardy-Weinberg equilibrium (HWE) (p < 0.001), and those having less than 5% missed calls, minor allele frequencies >5%, and Mendelian errors <1%. Note that because some SNPs may fail several criteria, the number of remaining SNPs is not equal to the total number of SNPs minus those removed in the pruning process.