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Table 2 Mean (and standard deviation) genotype concordance, genotype correlation and allele dosage correlation for validation animals in S1

From: Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle

  Genotype concordance rate Genotype correlation Dosage correlation
BEAGLE BSWa 0.964 (0.004) 0.829 (0.019) 0.945 (0.011)
FImpute BSW 0.953 (0.005) 0.766 (0.021)
IMPUTE2 BSW 0.971 (0.004) 0.872 (0.021) 0.956 (0.009)
Minimac BSW 0.972 (0.004) 0.872 (0.021) 0.959 (0.008)
BEAGLE Allb 0.967 (0.007) 0.840 (0.035) 0.965(0.010)
FImpute All 0.956 (0.008) 0.775 (0.038)
IMPUTE2 All 0.974 (0.007) 0.879 (0.035) 0.972 (0.009)
Minimac All 0.975 (0.007) 0.879 (0.035) 0.974 (0.008)
  1. aImputation accuracy evaluated for BSW validation animals only
  2. bImputation accuracy evaluated for all validation animals