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Table 3 Allele error rate (ER A , %), genotype error rate (ER G , %) and correlation (COR) between imputed and true genotypes for different sets of markers a in two datasets b

From: Genomic relationships based on X chromosome markers and accuracy of genomic predictions with and without X chromosome markers

Dataset Method ALL AUTO PAR X
ERA ERG COR ERA ERG COR ERA ERG COR ERA ERG COR
IMP_test Findhap 1.7 3.3 0.972 1.7 3.3 0.974 10.4 19.1 0.829 3.3 4.1 0.940
  Beagle 1.1 2.2 0.982 1.1 2.1 0.983 8.8 15.9 0.858 3.0 3.0 0.941
IMP_0.5ref Findhap 2.0 3.9 0.967 2.0 3.8 0.968 10.3 18.7 0.833 3.8 4.4 0.930
  Beagle 1.2 2.4 0.981 1.2 2.3 0.982 8.9 16.4 0.854 3.5 3.9 0.933
  1. aALL: all markers; AUTO: markers on the autosomes; PAR: markers on the pseudo-autosomal region; X: X-specific markers on the X chromosome; bIMP_test: for the test animals in genomic prediction, the 54K marker data were imputed from LD marker data; IMP_0.5ref: for half (randomly chosen) of the reference animals, the 54K marker data were imputed from LD marker data.