Skip to main content

Table 1 Genotype concordance metrics

From: Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

 

Genotype concordance

Non-reference sensitivity

 

GATK

Freebayes

SAMtools

GATK

Freebayes

SAMtools

 

No.SNPs

Mean ± SD

No.SNPs

Mean ± SD

No.SNPs

Mean ± SD

No.SNPs

Mean ± SD

No.SNPs

Mean ± SD

No.SNPs

Mean ± SD

≤0.1

23

0.03 ± 0.03

9

0.03 ± 0.03

3

0.08 ± 0.00

3

0.01 ± 0.02

9

0.04 ± 0.04

5

0.04 ± 0.04

≤0.2

18

0.14 ± 0.03

6

0.15 ± 0.03

6

0.15 ± 0.02

13

0.15 ± 0.03

10

0.14 ± 0.03

15

0.14 ± 0.03

≤0.3

12

0.25 ± 0.02

9

0.27 ± 0.02

9

0.25 ± 0.03

25

0.25 ± 0.03

7

0.24 ± 0.03

20

0.24 ± 0.03

≤0.4

13

0.33 ± 0.02

5

0.33 ± 0.01

18

0.35 ± 0.03

20

0.34 ± 0.02

11

0.34 ± 0.03

19

0.34 ± 0.03

≤0.5

22

0.45 ± 0.03

18

0.45 ± 0.03

24

0.45 ± 0.03

20

0.45 ± 0.02

14

0.45 ± 0.03

24

0.44 ± 0.03

≤0.6

42

0.55 ± 0.03

39

0.55 ± 0.04

43

0.55 ± 0.03

59

0.52 ± 0.03

89

0.51 ± 0.02

82

0.51 ± 0.03

≤0.7

73

0.65 ± 0.03

64

0.66 ± 0.03

62

0.66 ± 0.03

96

0.66 ± 0.02

105

0.66 ± 0.02

158

0.66 ± 0.03

≤0.8

110

0.76 ± 0.03

183

0.76 ± 0.03

123

0.76 ± 0.03

152

0.75 ± 0.02

150

0.75 ± 0.02

215

0.75 ± 0.02

≤0.9

679

0.87 ± 0.03

3828

0.88 ± 0.02

738

0.87 ± 0.03

1206

0.86 ± 0.03

1171

0.86 ± 0.03

1561

0.86 ± 0.03

≤1

50441

0.98 ± 0.02

46725

0.97 ± 0.02

50334

0.98 ± 0.02

49732

0.99 ± 0.02

49206

0.99 ± 0.02

49148

0.99 ± 0.02

 

Non-reference genotype concordance

Precision

≤0.1

55

0.02 ± 0.03

34

0.02 ± 0.03

35

0.02 ± 0.03

46

0.02 ± 0.04

28

0.01 ± 0.03

28

0.01 ± 0.03

≤0.2

18

0.13 ± 0.03

10

0.14 ± 0.03

23

0.14 ± 0.03

11

0.14 ± 0.03

12

0.15 ± 0.03

11

0.16 ± 0.03

≤0.3

24

0.26 ± 0.03

20

0.25 ± 0.03

24

0.25 ± 0.03

22

0.25 ± 0.03

22

0.25 ± 0.03

17

0.25 ± 0.03

≤0.4

32

0.34 ± 0.02

35

0.34 ± 0.02

43

0.35 ± 0.02

26

0.35 ± 0.03

21

0.34 ± 0.02

20

0.35 ± 0.03

≤0.5

32

0.43 ± 0.03

41

0.43 ± 0.03

38

0.43 ± 0.03

15

0.42 ± 0.02

36

0.43 ± 0.03

21

0.44 ± 0.03

≤0.6

144

0.52 ± 0.03

249

0.52 ± 0.03

168

0.52 ± 0.03

99

0.52 ± 0.03

161

0.52 ± 0.03

99

0.53 ± 0.03

≤0.7

245

0.66 ± 0.03

540

0.66 ± 0.03

297

0.65 ± 0.03

157

0.66 ± 0.03

499

0.66 ± 0.03

156

0.66 ± 0.03

≤0.8

445

0.75 ± 0.02

1725

0.76 ± 0.03

584

0.76 ± 0.02

270

0.75 ± 0.02

2246

0.76 ± 0.02

240

0.75 ± 0.02

≤0.9

3019

0.86 ± 0.03

6607

0.86 ± 0.03

3720

0.86 ± 0.03

1644

0.86 ± 0.03

6808

0.85 ± 0.03

1964

0.86 ± 0.03

≤1

47312

0.98 ± 0.03

41511

0.97 ± 0.03

46315

0.98 ± 0.03

49038

0.99 ± 0.02

40941

0.97 ± 0.03

48692

0.98 ± 0.03

  1. The calculation based on array genotypes and corresponding sequence-based genotypes obtained with different variant callers at positions where SNPs from the array were available on chromosomes 3, 6 and 28