Table 3 Mean (and standard deviation or range for cross validation scenarios) genotype concordance rate (Gen Conc), genotype correlation (Gen Corr), and allele dosage correlation (Dos Corr) between called sequence variants and imputed variants for animals in the validation set in scenarios S2 to S7

 Beagle

0.947 (0.024)

0.967 (0.013)

0.945

(0.94–0.95)

0.966

(0.96–0.972)

0.979

(0.976–0.981)

0.984

(0.983–0.986)

 FImpute

0.938 (0.024)

0.957 (0.012)

0.935

(0.93–0.944)

0.960

(0.953–0.965)

0.974

(0.971–0.977)

0.982

(0.98–0.984)

 IMPUTE2

0.962 (0.02)

0.973 (0.008)

0.959

(0.956–0.963)

0.9712

(0.966–0.975)

0.981

(0.978–0.983)

0.985

(0.984–0.987)

 Minimac

0.96 (0.02)

0.972 (0.008)

0.957

(0.955–0.962)

0.968

(0.963–0.973)

0.980

(0.978–0.983)

0.9852

(0.983–0.987)

 Beagle

0.863 (0.053)

0.914 (0.031)

0.857

(0.848–0.87)

0.914

(0.899–0.923)

0.932

(0.923–0.941)

0.932

(0.924–0.94)

 FImpute

0.827 (0.052)

0.879 (0.029)

0.819

(0.805–0.845)

0.894

(0.878–0.904)

0.916

(0.904–0.926)

0.923

(0.91–0.931)

 IMPUTE2

0.905 (0.042)

0.930 (0.02)

0.897

(0.891–0.908)

0.9261

(0.915–0.932)

0.939

(0.93–0.946)

0.938

(0.93–0.945)

 Minimac

0.899 (0.041)

0.926 (0.022)

0.8912

(0.886–0.902)

0.9162

(0.905–0.924)

0.9358

(0.927–0.944)

0.935

(0.927–0.943)

 Beagle

0.951 (0.028)

0.973 (0.013)

0.956

(0.951–0.961)

0.977

(0.972–0.979)

0.980

(0.978–0.982)

0.982

(0.98–0.983)

 FImpute

–

–

–

–

–

–

 IMPUTE2

0.964 (0.023)

0.977 (0.009)

0.967

(0.963–0.971)

0.979

(0.975–0.98)

0.980

(0.978–0.981)

0.981

(0.979–0.982)

 Minimac

0.964 (0.023)

0.978 (0.009)

0.967

(0.963–0.971)

0.9786

(0.975–0.98)

0.982

(0.98–0.983)

0.983

(0.981–0.984)