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Table 1 Mean number of heterozygote SNPs (per called SNP) in array and WGS low coverage data for 20 world populations

From: Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data

   

VARIANT CALLING

 
 

Ave N of Het. WGS

Ave N of Het. Array

Concor.

Discor.

He A − Ho W

Ho A − He W

ROH error

FIN

2,432,921.7

398,280.1

99.6929

0.3071

0.0402

0.2669

0.227

GBR

2,463,526.4

405,223.1

99.6898

0.3102

0.0430

0.2672

0.224

IBS

2,440,125.2

399,870.1

99.6547

0.3453

0.0412

0.3041

0.263

TSI

2,445,524.4

401,124.4

99.6015

0.3985

0.0424

0.3562

0.314

CEU

2,479,523.5

417,837.2

99.6365

0.3635

0.0402

0.3232

0.283

ACB

3,283,726.5

454,173.7

99.6723

0.3277

0.0403

0.2874

0.247

ASW

3,262,716.1

462,107.3

99.6526

0.3474

0.0448

0.3026

0.258

MXL

2,524,698.2

385,362.1

99.7197

0.2803

0.0433

0.2370

0.194

CLM

2,317,649.7

377,844.5

99.6716

0.3284

0.0460

0.2825

0.236

PEL

2,100,245.2

352,485.3

99.6987

0.3013

0.0411

0.2601

0.219

PUR

2,421,174.0

381,603.3

99.4125

0.5875

0.0448

0.5427

0.498

CDX

2,313,375.1

371,361.9

99.7197

0.2803

0.0351

0.2452

0.210

CHB

2,330,226.6

377,553.5

99.7197

0.2803

0.0366

0.2437

0.207

CHS

2,317,649.7

377,844.5

99.6991

0.3009

0.0451

0.2558

0.211

JPT

2,320,417.1

375,586.6

99.3659

0.6341

0.0354

0.5988

0.563

KHV

2,350,584.8

368,521.5

99.8549

0.1451

0.0343

0.1109

0.077

YRI

2,840,113.4

463,890.4

99.5746

0.4254

0.0383

0.3871

0.349

LWK

2,840,253.9

441,435.7

99.5545

0.4455

0.0457

0.3998

0.354

ZUL

2,840,578.1

441,536.6

98.7062

1.2938

0.6338

0.6600

0.026

BAG

2,840,658.6

441,412.3

99.2791

0.7209

0.3157

0.4052

0.090

  1. Concor. Concordant, Discor. Discordant
  2. He A – Ho W SNP called heterozygote by array and homozygote by WGS
  3. Ho A – He W SNP called homozygote by array and heterozygote by WGS
  4. ROH error % of SNPs that being wrongly called can break a ROH
  5. Mean variant calling concordance (in %) is shown. Discordance is discomposed in SNP called heterozygous by array but homozygous by WGS and vice versa. Finally a ROH error is defined as the % of SNP that according to variant calling discordance would break ROH in WGS low coverage data
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BMC Genomics

ISSN: 1471-2164

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