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Table 1 Call rate and genotyping error for two SNPs in high 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

99.75

99.75

99.75

0.05

0.05

0.05

M2

99.87

99.75

99.75

0.06

0.05

0.05

M3

99.87

99.82

99.80

0.04

0.05

0.05

  1. M1: the one-SNP-at-a-time method; M2: imputation based on estimated genotypes from M1 and LD structure; M3: our method that jointly analyzes the signal of two SNPs.