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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