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Table 3 Call rate and genotyping error for two SNPs in mixed quality

From: Genotype determination for polymorphisms in linkage disequilibrium

  

call rate (%)

error rate (%)

r 2

 

0.802

0.500

0.304

0.802

0.500

0.304

M1

SNP1

99.75

99.75

99.74

0.05

0.05

0.05

 

SNP2

97.96

97.98

97.97

0.54

0.54

0.53

M2

SNP1

99.87

99.75

99.74

0.06

0.05

0.05

 

SNP2

98.89

98.02

97.97

0.63

0.56

0.53

M3

SNP1

99.87

99.82

99.79

0.04

0.05

0.05

 

SNP2

98.81

98.37

98.19

0.30

0.43

0.49

  1. SNP1 was in high quality and SNP2 was in low quality.