The average genotype reproducibility in 25 replicate pairs across all passing SNPs was 99.94 %. Of the passing markers, 40,745 (7.00 %) were monomorphic, 17,099 (2.94 %) had minor allele frequency (MAF) greater than 0 and less than 0.01; 125,359 (21.53 %) had MAF between 0.01 and 0.05; 398,940 (68.53 %) had MAF greater than or equal to 0.05. For 137 HapMap samples [56] (45 JPT, 32 CEU, 60 YRI) and 226,511 passing markers that overlapped with HapMap2 release 24 (marker call rate ≥95 % in HapMap2), the average genotype concordance was 99.76 %.
