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Table 5 Evaluation of imputation accuracy

From: Imputation of high-density genotypes in the Fleckvieh cattle population

Number of animals in reference and validation population

Beagle

MaCH

findhap.f90

Minimac

Correct alleles

Correct genotypesa

rTG,IG

Correct alleles

Correct genotypes

rTG,IG

Correct alleles

Correct genotypes

rTG,IG

Correct alleles

Correct genotypes

rTG,IG

50 / 747

0.914

0.840

0.858

0.966

0.933

0.945

0.925

0.858

0.865

0.971

0.942

0.953

100 / 697

0.963

0.927

0.940

0.985

0.970

0.976

0.959

0.921

0.933

0.986

0.972

0.977

200 / 597

0.986

0.972

0.977

0.993

0.987

0.989

0.978

0.956

0.965

0.993

0.986

0.989

400 / 397

0.993

0.987

0.989

0.996

0.993

0.994

0.986

0.973

0.978

0.996

0.992

0.993

  1. The mean allelic and genotypic accuracies over six chromosomes (BTA1, BTA5, BTA10, BTA15, BTA20, BTA25) were assessed for the imputed genotypes based on an increasing size of the reference population. Additionally, the correlation between true and imputed genotypes (rTG,IG) was calculated.
  2. a a genotype is correctly imputed if both alleles are correctly imputed.