Table 2 Mean and standard deviation (SD) of correlation between true and imputed genotype dosage for Holstein (HOL), Jersey (JER) and Nordic Red (RDC)

BEAGLE/BEAGLE pre-phasing (Single breed)

0.87

0.32

0.82

0.38

0.76

0.39

BEAGLE/BEAGLE pre-phasing

0.88

0.32

0.87

0.32

0.86

0.30

BEAGLE/SHAPEIT2 pre-phasing

0.88

0.30

0.86

0.32

0.85

0.30

BEAGLE/Genotype probabilities

0.90

0.27

0.89

0.28

0.87

0.27

IMPUTE2/BEAGLE pre-phasing

0.90

0.20

0.85

0.23

0.86

0.20

IMPUTE2/SHAPEIT2 pre-phasing

0.90

0.20

0.84

0.23

0.86

0.21

IMPUTE2/Genotype probabilities

0.90

0.20

0.84

0.22

0.87

0.18