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Table 5 Mean and standard deviation (SD) of concordance rate and allelic R 2 calculated for different algorithms, panel densities and scenarios for both imputation to 50K and 777K SNP panels

From: Accuracy of genome-wide imputation in Braford and Hereford beef cattle

   CR Allelic R 2
  No. Mean SD Mean SD
   Imputation to the 50K SNP panel
Algorithm   
Beagle 10 0.927 0.042 0.890 0.067
Fimpute 20 0.943 0.038 0.912 0.061
Panel   
3K 6 0.864 0.011 0.787 0.016
6K 6 0.946 0.008 0.919 0.011
8K 6 0.952 0.008 0.927 0.011
15K 6 0.973 0.006 0.962 0.008
20K 6 0.953 0.008 0.929 0.011
Scenario   
NE-P 5 0.943 0.041 0.913 0.065
NE-NP 10 0.935 0.041 0.901 0.066
NNE-P 5 0.943 0.042 0.912 0.067
NNE-NP 10 0.935 0.042 0.901 0.066
   Imputation to the 777K SNP panel
Algorithm   
Beagle 8 0.895 0.040 0.826 0.066
Fimpute 16 0.921 0.035 0.866 0.059
Panel   
3K1 3 0.838 0.017 0.728 0.025
6K1 3 0.898 0.016 0.829 0.025
8K1 3 0.902 0.017 0.836 0.026
15K1 3 0.918 0.017 0.863 0.027
20K1 3 0.903 0.017 0.837 0.026
50K 3 0.930 0.016 0.882 0.025
90iK 3 0.952 0.010 0.919 0.016
90tK 3 0.955 0.009 0.925 0.014
Scenario   
NE-P 8 0.9199 0.037 0.865 0.062
NE-NP 16 0.9082 0.039 0.846 0.065
Step   
One-step 15 0.8064 0.884 0.674 0.147
Two-step 15 0.8920 0.032 0.819 0.053
  1. 1Means and standard deviation for the two-step analysis.