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Table 2 Variation detection and annotation

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

  

Hiseq-1

Hiseq-2

Hiseq-3

Hiseq-4

BGISEQ-1

BGISEQ-2

BGISEQ-3

BGISEQ-4

SNV

total number a

41,554

41,506

41,627

41,540

41,264

41,294

41,292

41,172

found in dbSNP(%)

99.75

99.73

99.70

99.78

99.74

99.76

99.76

99.80

homozygous

15,741

15,723

15,723

15,758

15,671

15,666

15,692

15,642

heterozygous

25,813

25,783

25,904

25,782

25,593

25,628

25,600

25,530

Ti/Tv

2.56

2.57

2.56

2.56

2.56

2.56

2.56

2.56

het/hom b

1.64

1.64

1.65

1.64

1.63

1.64

1.63

1.63

intronic variations c

17,298

17,351

17,321

17,288

17,217

17,232

17,220

17,229

exonic variations

21,540

21,497

21,561

21,533

21,408

21,407

21,433

21,322

coding variations

19,353

19,332

19,354

19,364

19,269

19,273

19,291

19,210

nonsynonmous

9446

9439

9437

9466

9393

9391

9400

9343

Ti/Tv on exome

3.09

3.10

3.08

3.09

3.08

3.08

3.08

3.09

het/hom on exome

1.52

1.52

1.52

1.52

1.52

1.52

1.52

1.52

indel

total number

3461

3436

3470

3445

3503

3559

3506

3538

found in dbSNP(%)

94.42

95.08

94.55

94.83

94.78

94.44

94.69

94.04

homozygous

1491

1491

1492

1502

1433

1444

1432

1420

heterozygous

1970

1945

1978

1943

2070

2115

2074

2118

het/hom

1.32

1.30

1.33

1.29

1.44

1.46

1.45

1.49

intronic variations

2493

2493

2518

2496

2558

2585

2553

2581

exonic variations

703

689

702

694

705

706

703

702

coding variations

460

465

459

464

473

477

468

473

het/hom on exome

1.12

1.11

1.11

1.11

1.17

1.21

1.14

1.17

  1. aOnly variants on target region were used in these statistics
  2. bhet/hom, heterozygous to homozygous variation ratio
  3. cVariations located at splicing sites are considered as nonsynonymous and not count as intronic