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Table 3 Mean allelic error rate of imputing SNP genotypes between different SNP chips obtained with IMPUTE2

From: Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle

Scenario

Animals masked (%)

N animals total

N animal reference

N animals test

N SNP

N

%

Mean allelic error rate (%)

snp

snp

masked

masked

15K by 50K

25

1419

1065

354

1529

205

13

0.80

50

1419

710

709

1529

205

13

0.95

75

1419

355

1064

1529

205

13

1.40

50K by 15K

25

1419

1065

354

1529

1324

87

2.85

50

1419

710

709

1529

1324

87

3.15

75

1419

355

1064

1529

1324

87

4.25

25K by 50K

25

431

324

107

1652

328

20

1.50

50

431

216

215

1652

328

20

1.85

75

431

108

323

1652

328

20

2.75

50K by 25K

25

431

324

107

1652

1324

80

2.75

50

431

216

215

1652

1324

80

2.75

75

431

108

323

1652

1324

80

4.55

  1. The results are shown for three SNP chips viz. 15K, 25K and 50K and chromosome 20.