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Table 1 Description of the three twin pairs and corresponding sequencing statistics

From: Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease

 

Twin pair 1

Twin pair 2

Twin pair 3

Sex

Female

Female

Female

Age of onset in affected twin

45

19

12

Year of birth

1944

1962

1974

Recruited

2007

2007

2006

Last recontact

2008

2007

2012

 

Genomes

Exomes

Exomes

 

Blood CD

Biopsy CD

Blood healthy

Biopsy healthy

Blood CD

Biopsy CD

Blood healthy

Biopsy healthy

Blood CD

Blood healthy

Blood CD

Blood healthy

Gb coverage

126.70

124.02

143.82

110.28

3.44

3.16

2.47

3.50

3.33

3.29

2.86

2.21

Average coverage

41.92

41.03

47.58

36.49

55.36

50.83

39.81

56.34

72.29

71.58

62.22

47.88

% of genome/exome covered:

            

≥ 1×

93.12

93.05

93.04

93.03

97.10

97.17

96.25

96.97

97.28

97.16

96.64

95.36

≥ 8×

90.46

88.95

88.77

90.49

91.48

90.72

89.11

91.82

90.13

89.87

88.91

85.25

≥ 20×

73.29

65.11

67.26

80.82

83.37

79.47

76.78

84.72

80.39

79.87

78.27

71.02

Total number of variants

3,064,772

3,053,010

3,055,001

3,081,680

44,890

44,357

44,928

44,920

29,180

28,985

28,407

27,465

Ti/Tv ratio

2.1

2.1

2.1

2.1

2.6

2.6

2.6

2.6

2.7

2.7

2.7

2.8

NS/S ratio

0.9

0.9

0.9

0.9

0.8

0.8

0.8

0.8

0.9

0.9

0.9

0.9

Total number of SNVs

2,894,614

2,878,835

2,877,807

2,911,350

44,377

43,846

44,426

44,406

28,663

28,542

27,947

27,185

Total number of InDels

170,158

174,175

177,194

170,330

514

512

503

515

517

443

460

280

Synonymous SNVs

9,655

9,630

9,658

9,625

10,168

10,046

10,163

10,205

8,977

8,920

8,678

8,457

Missense SNVs

8,443

8,414

8,425

8,413

8,600

8,488

8,588

8,618

7,668

7,639

7,562

7,369

Nonsense SNVs

64

66

63

65

57

56

57

57

56

58

58

54

Non-frameshift InDels

77

76

78

78

208

208

201

209

205

182

169

111

Frameshift InDels

53

48

54

48

144

142

141

143

296

246

273

162

Stopgain InDels

0

0

0

0

3

3

3

3

0

0

0

0

Splice-site variants

55

56

56

58

96

96

96

98

45

45

49

34

Variants in UTR

208,685

207,740

207,924

209,726

23,714

23,446

23,770

23,685

1,253

1,241

1,195

1,143

Intronic variants

956,711

953,878

954,959

962,132

1,659

1,635

1,667

1,659

10,154

10,127

9,836

9,573

Intergenic variants

1,881,029

1,873,102

1,873,784

1,891,535

242

238

243

244

526

527

587

562

Novel SNVs

54,823 (1.9%)

54,251 (1.9%)

54,372 (1.9%)

55,243 (1.9%)

988 (2.2%)

988 (2.3%)

960 (2.2%)

995 (2.2%)

2,009 (7.0%)

2,023 (7.1%)

1,802 (6.4%)

1,724 (6.3%)

Damaging SNV predictions

            

HGMD

57

59

55

59

61

61

61

61

44

43

40

41

SIFT

697

689

697

695

685

686

683

689

674

670

645

630

PolyPhen2

734

731

728

733

765

764

755

767

653

651

648

639

Grantham score

1,442

1,437

1,445

1,439

1,496

1,499

1,477

1,501

1,356

1,355

1,372

1,327

PhyloP

7,753

7,728

7,730

7,757

1,854

1,855

1,837

1,859

1,968

1,964

1,957

1,892

  1. Coverage and variant calls for exomes refer to the corresponding exome target. Ti/Tv ratio: transition/transversion ratio of SNVs; NS/S ratio: nonsynonymous to synonymous ratio of SNVs; SNVs not in dbSNP132 for TP1 (hg19) and dbSNP130 for TP2 and TP3 (hg18) are defined as novel. SNVs predicted to be damaging: “DM” in HGMD (Human Gene Mutation Database Professional, version 2013.3), missense SNVs called as “deleterious” by SIFT, “probably damaging” by PolyPhen2, grantham score above 100 or positions with a phyloP value above 2.5.