Table 2 Individual variant load in coding regions.

From: Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

Variant type

Population

Very-rare (<0.1%)

Rare (0.1–0.5%)

Low (0.5–5%)

Common (>5%)

Total

  

Mean

s.d.

Mean

s.d.

Mean

s.d.

Mean

s.d.

Mean

s.d.

Heterozygous

 HGMD-DM*

1KJPN (1,070) high confidence

0.640

0.814

1.039

1.016

4.757

2.246

3.179

1.604

9.619

3.032

 

1KJPN (1,070) high-sensitive

0.675

0.848

1.107

1.051

4.905

2.261

4.388

1.787

11.074

3.136

 

1KGP JPT (89)

NA

NA

NA

NA

6.270

2.503

4.169

1.829

10.438

2.969

 

1KGP CHB (97)

NA

NA

NA

NA

5.536

2.381

4.464

1.921

10.000

3.218

 

1KGP CHS (100)

NA

NA

1.470

1.359

4.320

2.049

3.680

1.803

9.470

2.798

 Stop-gained

1KJPN (1,070) high-confidence

2.385

1.550

1.563

1.294

8.679

2.486

29.017

4.327

41.644

5.358

 

1KJPN (1,070) high-sensitive

2.624

1.616

1.777

1.376

6.008

2.402

42.125

4.878

52.535

5.795

 

1KGP JPT (89)

NA

NA

NA

NA

8.685

2.987

39.337

5.261

48.022

6.166

 

1KGP CHB (97)

NA

NA

NA

NA

9.742

3.215

37.845

5.593

47.588

6.777

 

1KGP CHS (100)

NA

NA

3.860

2.433

6.580

3.085

36.070

4.860

46.510

5.947

Homozygous

 HGMD-DM*

1KJPN (1070) high-confidence

0.001

0.031

0.003

0.053

0.048

0.230

1.570

1.126

1.621

1.145

 

1KJPN (1,070) high-sensitive

0.000

0.000

0.003

0.053

0.050

0.234

1.862

1.235

1.914

1.251

 

1KGP JPT (89)

NA

NA

NA

NA

0.022

0.149

1.899

1.244

1.921

1.227

 

1KGP CHB (97)

NA

NA

NA

NA

0.052

0.222

2.021

0.989

2.072

1.003

 

1KGP CHS (100)

NA

NA

0.000

0.000

0.000

0.000

0.000

0.000

2.110

1.118

 Stop-gained

1KJPN (1,070) high-confidence

0.005

0.081

0.004

0.061

0.753

0.747

11.303

2.713

12.064

2.813

 

1KJPN (1,070) high-sensitive

0.008

0.101

0.008

0.101

0.099

0.302

12.101

2.853

12.217

2.851

 

1KGP JPT (89)

NA

NA

NA

NA

0.067

0.252

11.315

2.898

11.382

2.914

 

1KGP CHB (97)

NA

NA

NA

NA

0.052

0.222

12.093

2.758

12.144

2.769

 

1KGP CHS (100)

NA

NA

0.000

0.000

0.070

0.326

12.900

3.047

12.970

3.096

  1. CHB, Han Chinese in Beijing, China; CHS , Han Chinese South, China; HGMD, Human Gene Mutation Database; JPT, Japanese in Tokyo, Japan; 1KGP, 1000 Genomes Project; 1KJPN, reference panel of 1,070 Japanese individual; NA, not available; ORF, open reading frame; SNV, single-nucleotide variant.
  2. SNV sites with reliable ancestral states were used.
  3. *HGMD-DM (disease-causing) alleles were analysed if they are derived alleles and alternative (non-reference) alleles.
  4. We selected stop-gained alleles if they are derived alleles and alternative (non-reference) alleles. We discarded stop-gained SNVs if the proportion of truncated ORF is less than 5%.