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Table 3 Number of SNP used for the evaluation of imputation accuracy on six chromosomes

From: Imputation of high-density genotypes in the Fleckvieh cattle population

Chr

Chromosome-length [Mb]

Number of high-density SNP in the reference population

Average distance between two high-density SNP [bp]

Number of medium-density SNP in the validation population

Average distance between two medium-density SNP [bp]

1

158.32

39 167

4042

2568

61 587

5

121.18

29 050

4171

1621

74 740

10

104.30

26 695

3906

1646

62 724

15

85.27

21 425

3978

1280

65 850

20

71.98

19 111

3764

1183

60 530

25

42.85

11 725

3648

744

57 533

  1. Number of high-density SNP passing stringent quality parameters for the six evaluated chromosomes. The medium-density SNP are a subset of the bovineHD BeadChip collection that are interrogated with the BovineSNP50 BeadChip (version 2). SNP positions were determined based on the UMD3.1 assembly of the bovine genome.