Table 2 SNP-calling results from clinical and HapMap samples using GENCODE and Agilent CCDS exome captures

From: The GENCODE exome: sequencing the complete human exome

Sample name

Sanger no. 1

Sanger no. 2

Sanger no. 3

Sanger no. 4

Sanger no. 5

Sanger no. 6

Sanger no. 7

NA12878

NA07000

NA19240

NA12878

NA07000

NA19240

Bait library

GENCODE exome

Agilent CCDS

SNPs (polymorphic sites only)

21 170

21 529

21 052

21 445

21 124

23 612

23 276

20 780

21 513

24 520

16 732

17 014

21 915

dbSNP, % (version 130)

93.7

93.5

93.7

93.8

92.1

93.5

93.5

96.5

94.1

94.8

98.0

95.2

95.5

dbSNP/1000G, % (26/03/10 pilot 1)

96.3

95.1

96.3

96.1

94.7

96.1

96.1

97.7

97.2

97.3

99.0

97.9

98.1

Hets

12 604

13 241

12 938

13 153

13 297

14 476

14 321

12 675

13 588

16 121

10 094

10 583

14 414

Ti/Tv

3.029

2.996

3.036

3.025

2.930

3.021

3.120

3.069

3.112

3.138

3.235

3.258

3.322

Concordanta

4638/4648

4706/4716

4649/4654

4569/4582

4639/4652

5204/5213

b

10 491/10 564

10 862/10 904

10 720/10 810

8850/8909

9057/9088

9795/9877

Concordant %

99.78

99.79

99.89

99.72

99.72

99.83

b

99.31

99.61

99.16

99.34

99.66

99.17

Synonymous

9196

9249

9072

9191

8948

10 220

10 111

8480

9207

10 568

7979

8133

10 528

Synonymous/Mb (35.2 Mb)

261.25

262.76

257.73

261.11

254.21

290.35

287.25

240.91

261.57

300.23

226.68

231.05

299.10

Non-synonymous

8608

8804

8692

8828

8696

9634

9385

8758

8703

9958

6863

6976

8918

Non-synonymous/ Mb (35.2 Mb)

244.55

250.12

246.94

250.80

247.05

273.70

266.62

248.81

247.25

282.90

194.97

198.18

253.36

Stop gained

86

85

80

89

128

87

95

80

83

99

44

40

51

Stop gained/Mb (35.2 Mb)

2.44

2.41

2.27

2.53

3.64

2.47

2.70

2.27

2.36

2.81

1.25

1.14

1.45

SNPs (polymorphic sites only) – within GENCODE-only ECRsc

5179

5212

5117

5162

5162

5414

5424

5017

5319

5887

   

SNPs (polymorphic sites only) – within GENCODE-only ECRs/Mbc

691.77

696.17

683.48

689.50

689.50

723.16

724.49

670.13

710.47

786.33

   
  1. aConcordant SNPs were compared with Illumina 660K chip GenCall genotypes for clinical samples or HapMap3 genotypes for HapMap samples NA12878, NA07000 and NA19240.
  2. bMissing data.
  3. cExcluding flanking regions.
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