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

From: Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle

METHOD HOL JER RDC
  Mean SD Mean SD Mean SD
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