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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

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

Gen Conc S2 S3 S4 S5 S6 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)
Geno Corr
 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)
Dos Corr
 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)