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Table 1 Different quality measures of the estimated line B proportions derived with ADMIXTURE with various levels of pruning based on linkage disequilibrium (r2) in the simulated dataa

From: Estimation of dam line composition of 3-way crossbred animals using genomic information

Measure

Lines

r2 threshold for pruning

0.1

0.3

0.5

0.7

0.9

No.

Number of SNPs

Close

305

1364

2661

3781

4679

5720

Distant

281

1190

2425

3543

4499

5753

Unrelated

260

936

1953

3016

3989

5740

Accuracy

Close

0.560

0.694

0.696

0.689

0.682

0.675

Distant

0.787

0.890

0.901

0.897

0.890

0.886

Unrelated

0.891

0.958

0.966

0.965

0.963

0.959

Dispersion bias

Close

0.404

0.533

0.536

0.531

0.524

0.517

Distant

0.653

0.808

0.824

0.820

0.809

0.801

Unrelated

0.810

0.916

0.930

0.930

0.925

0.922

Maximum error

Close

0.404

0.330

0.332

0.334

0.341

0.348

Distant

0.285

0.192

0.181

0.181

0.186

0.190

Unrelated

0.181

0.110

0.104

0.103

0.109

0.112

RMSE

Close

0.132

0.106

0.106

0.107

0.108

0.109

Distant

0.083

0.056

0.053

0.054

0.056

0.058

Unrelated

0.056

0.034

0.031

0.031

0.032

0.034

  1. RMSE root mean squared error
  2. aAll 428 A(BC) crossbreds were used