Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation

BMC Genomics

Table 1 The number of SNPs used for calculations in each HapMap population sample

	YRI	CEU	ASI
All genotyped SNPs in regions	4540	4670	4495
Post validation markers:
MAF = 1%
minGeno ≥ 95%	3085	2293	2164
hwCutoff ≥ 0.001
Post validation markers:
MAF = 5%
minGeno = 95%	2438	1912	1991
hwCutoff = 0.001

The number of SNPs genotyped and the numbers of SNPs that passed validation criteria are shown. YRI, CEU and ASI (CHB + JPT) are, respectively, the Yoruban, CEPH and Asian (Chinese and Japanese) population samples from the HapMap data for two ENCODE regions of chromosome 2. MAF – minor allele frequency; minGeno – percentage of SNPs genotyped; hwCutoff – the p-value of the hypothesis that the current SNP is not in the Hardy-Weinberg Equilibrium.

ISSN: 1471-2164