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Table 1 Comparison of statistical performance of SNVHMM with SNVMix2 with different mapping quality (MQ) and base quality (BQ) threshold for 10X data

From: SNVHMM: predicting single nucleotide variants from next generation sequencing

Model

MQ

BQ

TP

FP

TN

FN

Sensitivity(%)

Specificity(%)

Accuracy(%)

F-score

SNVHMM

50

20

247

59

133

58

80.98

69.27

76.46(MVC = 4)

0.8085

40

20

254

66

126

51

83.28

65.63

76.46(MVC = 4)

0.8128

30

20

256

70

112

49

83.93

65.54

76.05(MVC = 4)

0.8114

30

10

236

63

129

69

77.38

67.19

73.44(MVC = 5)

0.7815

20

10

273

111

81

32

89.51

42.19

71.23(MVC = 3)

0.7925

10

5

273

110

82

32

89.51

42.71

71.43(MVC = 2)

0.7936

SNVMix2_TI

50

20

303

160

32

2

99.34

16.67

67.40

0.7891

40

20

305

174

18

0

100

9.38

64.99

0.7781

30

20

305

174

18

0

100

9.38

64.99

0.7781

30

10

305

173

19

0

100

9.89

65.19

0.7791

20

10

305

191

1

0

100

0.52

61.56

0.7615

10

5

305

192

0

0

100

0

61.37

0.7606

SNVMix2_TO

50

20

245

75

117

60

80.32

60.94

72.84

0.7840

40

20

261

88

104

44

85.57

54.17

73.44

0.7982

30

20

266

90

102

39

87.21

53.13

74.04

0.8048

30

10

274

92

100

31

89.83

52.08

75.25

0.8167

20

10

283

125

67

22

92.78

34.90

70.42

0.7938

 

10

5

290

134

58

15

95.08

30.21

70.02

0.7956