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Table 2 Pairwise concordance of genotype calls between Sanger and array-based methods

From: Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

 

Sanger

MouseDivGeno

AA

BB

Deleted

Inaccessible

Excluded

Total

AA

5,488,489

5,327

88

4,818

3,504

5,502,226

AB

51,460

39,080

24

424

1,316

92,304

BB

7,244

1,627,823

181

3,022

6,230

1,644,500

V

13,510

15,488

24

2,221

4,361

35,604

N

43,605

48,659

19

577

1,588

94,448

Total

5,604,308

1,736,377

336

11,062

16,999

7,369,082

Alchemy

AA

BB

Deleted

Inaccessible

Excluded

Total

AA

5,441,864

3,604

87

4,612

3,262

5,453,429

AB

97,883

46,767

34

553

1,741

146,978

BB

6,582

1,644,208

141

2,231

4,314

1,657,476

N

57,979

41,798

74

3,666

7,682

111,199

Total

5,604,308

1,736,377

336

11,062

16,999

7,369,082

BRLMM-P 2D

AA

BB

Deleted

Inaccessible

Excluded

Total

AA

5,523,440

7,022

63

4,673

3,456

5,538,654

AB

30,970

54,075

70

2,097

4,839

92,051

BB

7,702

1,631,208

169

2,509

5,164

1,646,752

N

42,196

44,072

34

1,783

3,540

91,625

Total

5,604,308

1,736,377

336

11,062

16,999

7,369,082