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Table 3 Variation accuracy estimation by comparison with GIAB

From: A new massively parallel nanoball sequencing platform for whole exome research

 

detected variants

GIAB-specific variations

Sensitivity (%)

Precision (%)a

F-measure (%)b

total

in GIAB

not in GIAB

SNV

Hiseq-1

35,051

34,851

200

359

98.98

99.43

99.20

 

Hiseq-2

35,026

34,793

233

417

98.82

99.33

99.07

 

Hiseq-3

35,030

34,821

209

389

98.90

99.40

99.15

 

Hiseq-4

35,037

34,842

195

368

98.95

99.44

99.20

 

BGISEQ-1

35,073

34,883

190

327

99.07

99.46

99.26

 

BGISEQ-2

35,069

34,876

193

334

99.05

99.45

99.25

 

BGISEQ-3

35,071

34,886

185

324

99.08

99.47

99.28

 

BGISEQ-4

35,048

34,881

167

329

99.07

99.52

99.29

 

Hiseq-1 PE100

35,110

34,905

205

305

99.13

99.42

99.27

 

Hiseq-2 PE100

35,056

34,855

201

355

98.99

99.43

99.21

 

Hiseq-3 PE100

35,174

34,880

294

330

99.06

99.16

99.11

 

Hiseq-4 PE100

35,143

34,897

246

313

99.11

99.30

99.21

indel

Hiseq-1

2501

2453

48

197

92.57

98.08

95.24

 

Hiseq-2

2493

2454

39

196

92.60

98.44

95.43

 

Hiseq-3

2507

2457

50

193

92.72

98.01

95.29

 

Hiseq-4

2508

2453

55

197

92.57

97.81

95.11

 

BGISEQ-1

2542

2480

62

170

93.58

97.56

95.53

 

BGISEQ-2

2571

2498

73

152

94.26

97.16

95.69

 

BGISEQ-3

2553

2478

75

172

93.51

97.06

95.25

 

BGISEQ-4

2564

2488

76

162

93.89

97.04

95.44

 

Hiseq-1 PE100

2538

2498

40

152

94.26

98.42

96.30

 

Hiseq-2 PE100

2512

2471

41

179

93.25

98.37

95.74

 

Hiseq-3 PE100

2541

2474

67

176

93.36

97.36

95.32

 

Hiseq-4 PE100

2523

2484

39

166

93.74

98.45

96.04

  1. aPrecision = true positive/(true positive + false positive). Precision instead of specificity was used because true negative dominate the region thus specificity is very close to 1
  2. bF-measure is the harmonic average of the sensitivity and precision. It combines sensitivity and precision in a single measurement