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Table 2 Comparisons of call rates and concordance on HapMap samples for rare variants under 600, 1500, and 3000 simulated observations and the allocation design 2:1

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

SNPs

# SNP

Item

M3-S

M3-S

M3-S

 
   

600

1500

3000

 

MAF < 0.1

4364

Call Rate

99.69

99.65

99.59

 
  

Accuracy

99.33

99.24

99.22

 

MAF < 0.05

2329

Call Rate

99.72

99.71

99.68

 
  

Accuracy

99.34

99.26

99.28

 

MAF < 0.01

597

Call Rate

99.59

99.86

99.81

 
  

Accuracy

99.04

99.06

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
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BMC Bioinformatics

ISSN: 1471-2105

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