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Table 3 Concordance of best-guess genotype calls from sequence data with SNP array genotypes, using allele read counts obtained with the default settings of GATK HaplotypeCaller

From: Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing

 

na

Genotype concordance (%)

Allele concordance (%)

Concordance by genotype (%)

True = 0

True = 1

True = 2

0|0

1|0

2|0

0|1

1|1

2|1

0|2

1|2

2|2

Low coverage

 1×

27,185

42.2

61.0

99.97

0.03

95.14

4.86

81.96

18.04

 2×

33,638

57.2

76.0

99.94

0.00

0.06

72.87

3.51

23.62

20.07

0.25

79.68

 3×

24,789

70.3

84.5

99.91

0.08

0.01

56.37

31.87

11.76

6.23

1.45

92.32

 4×

14,015

79.7

89.6

99.85

0.13

0.02

43.11

51.44

5.46

2.14

1.69

96.16

 5×

6502

85.6

92.7

99.93

0.04

0.04

32.65

64.75

2.59

0.90

1.96

97.14

 6–10×

3705

90.5

95.2

99.83

0.12

0.06

22.47

74.68

2.85

0.61

1.07

98.32

 Overall

109,834

62.1

77.6

99.92

0.04

0.03

66.41

21.50

12.09

29.84

0.71

69.45

High coverage

131,806

99.7

99.9

99.80

0.19

0.01

0.21

99.72

0.07

0.17

0.16

99.68

  1. aNumber of genotypes called across 26 individuals at 5136 and 5531 SNPs for low- and high-coverage data, respectively
  2. Concordance is shown by coverage at variant site