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Table 3 Comparisons of call rates and concordance on HapMap samples for rare variants among GenCall, GenoSNP, M3 and M3-S

From: M3-S: a genotype calling method incorporating information from samples with known genotypes

SNPs # SNP Item GenCall GenoSNP M3 M3-S
MAF < 0.1 4364 Call Rate 95.89 99.02 99.70 99.59
   Accuracy 95.65 98.28 99.19 99.22
MAF < 0.05 2329 Call Rate 96.44 98.89 99.64 99.68
   Accuracy 96.15 98.02 99.08 99.28
MAF < 0.01 597 Call Rate 94.37 98.90 99.53 99.81
   Accuracy 93.89 97.28 98.60 99.23
  1. Note: M3-S: M3 incorporating samples with known genotypes; Call Rate: the percentage of valid genotypes; Accuracy: the percentage of consistent genotype; # SNP: the number of SNPs whose MAFs are less than 0.1, 0.05 or 0.01, respectively