Table 2 Imputed SNPs in CONVERGE.

From: RETRACTED ARTICLE: 11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project

Chr

All Imputed

Known in 1000 Genomes Phase 1 ASN Panel

Novel in CONVERGE

Used in GWAS

  

Imputed

CONVERGE

Not in CONVERGE

% of Imputed

Count

% of Imputed

Count

% of Imputed

   

Count

(%)

Count

(%)

     

chr1

1906566

1049943

709178

67.54

340765

32.456

55.07

856623

44.93

473126

24.82

chr2

2080626

1141277

768281

67.32

372996

32.682

54.85

939349

45.15

504269

24.24

chr3

1730976

971680

660330

67.96

311350

32.042

56.14

759296

43.87

444601

25.69

chr4

1683635

963695

655100

67.98

308595

32.022

57.24

719940

42.76

452165

26.86

chr5

1552865

866733

586899

67.71

279834

32.286

55.82

686132

44.19

395356

25.46

chr6

1542585

895135

602872

67.35

292263

32.65

58.03

647450

41.97

416919

27.03

chr7

1386630

780333

519815

66.62

260518

33.385

56.28

606297

43.72

357113

25.75

chr8

1352488

743135

500602

67.36

242533

32.636

54.95

609353

45.05

330591

24.44

chr9

1049711

587643

394219

67.09

193424

32.915

55.98

462068

44.02

264762

25.22

chr10

1204931

669919

456560

68.15

213359

31.848

55.6

535012

44.4

310998

25.81

chr11

1203686

662829

443108

66.85

219721

33.149

55.07

540857

44.93

297679

24.73

chr12

1141658

644071

435882

67.68

208189

32.324

56.42

497587

43.59

294448

25.79

chr13

858815

486316

334096

68.7

152220

31.301

56.63

372499

43.37

225668

26.28

chr14

793487

445316

303662

68.19

141654

31.81

56.12

348171

43.88

201734

25.42

chr15

722748

397917

266748

67.04

131169

32.964

55.06

324831

44.94

175810

24.33

chr16

793223

418892

276272

65.95

142620

34.047

52.81

374331

47.19

178608

22.52

chr17

674848

363982

238795

65.61

125187

34.394

53.94

310866

46.07

150405

22.29

chr18

683315

386244

265213

68.67

121031

31.335

56.53

297071

43.48

173158

25.34

chr19

542027

299517

192281

64.2

107236

35.803

55.26

242510

44.74

128700

23.74

chr20

552234

294881

200864

68.12

94017

31.883

53.4

257353

46.6

127726

23.13

chr21

324063

182937

123793

67.67

59144

32.33

56.45

141126

43.55

83062

25.63

chr22

334001

180274

119161

66.1

61113

33.9

53.98

153727

46.03

79845

23.91

chrX

943020

404837

265078

65.48

139759

34.522

42.93

538183

57.07

175876

18.65

Total

25058138

13837506

9318809

67.35

4518697

32.655

55.22

11220632

44.78

6242619

24.91

  1. This table shows the number of imputed SNPs in CONVERGE in each chromosome. The first two columns show the chromosome and total number of SNPs imputed in that chromosome. The next six columns show the composition of these SNPs in relation to the 1000 Genomes Phase 1 ASN Panel: the number of SNPs imputed that were found to be polymorphic in 1000 Genomes Phase 1 ASN Panel, the number and percentage of SNPs polymorphic in CONVERGE, the number and percentage of SNPs not polymorphic in CONVERGE, and the percentage of SNPs in 1000 Genomes Phase 1 ASN Panel among all imputed SNPs. The following two columns show the number and percentage of imputed SNPs that were novel in CONVERGE. The final two columns show the number and percentage of imputed SNPs that were included in the GWAS for MDD.
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