Table 1 Number of different types of autosomal sequence variants detected in 49 Original Braunvieh cattle using three sequence variant genotyping methods (Full) and subsequent variant filtration based on commonly used criteria (Filtered)

Variants

21,140,196

20,262,913

20,668,459

19,761,679

17,679,155

18,871,549

SNPs

18,594,182

18,120,724

17,592,038

17,248,593

15,777,446

16,272,917

Not in dbSNP

1,387,781

1,505,586

882,575

867,838

564,326

570,901

Biallelic

18,347,962

18,053,396

17,528,249

17,111,806

15,730,153

16,218,714

Multi-allelic

246,220

67,328

63,789

136,787

47,293

54,203

Ti/Tv ratio

2.09

2.07

2.05

2.17

2.18

2.16

SNP array (%)

BovineHD

99.46

99.61

99.32

99.21

98.79

98.85

Bovine SNP50

99.14

99.26

99.12

98.91

98.87

98.90

Indels

2,478,489

2,044,585

3,076,421

2,445,766

1,826,808

2,598,632

Not in dbSNP

663,831

596,137

1,279,162

639,219

456,752

979,291

Biallelic

2,166,352

1,753,391

2,704,413

2,133,840

1,571,195

2,310,386

Multi-allelic

312,137

291,194

372,008

311,926

255,613

288,246

Insertion/Deletion

0.88

0.88

1

0.88

0.88

0.99

Complex variation

67,525

97,604

0

67,320

74,901

0