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Table 1 Accuracy of imputation using tagSNP selected for different values of r t 2 on chromosome 12

From: Genotype imputation accuracy in a F2 pig population using high density and low density SNP panels

rt2

Number of tagSNP

Number of SNP genomewide

Average distance between SNP (Mb)

Imputation accuracy ( IA)

0.1

33

1295

1.86

0.960

0.2

79

3100

0.79

0.970

0.3

158

6199

0.40

0.976

0.4

266

10436

0.24

0.980

0.5

399

15654

0.16

0.982

  1. r t 2 = Threshold of LD in statistical selection, Number of tagSNP = Number of SNP selected for a particular r t 2, Number of SNP Genomewide = The equivalent number of SNP that are needed genome-wide to keep the same average inter-marker distance. Average distance between SNP (Mb) = Average distance between tagSNP selected, Imputation accuracy (IA) = Imputation accuracy of non-tagSNP. Results using simulated data.