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. 2018 Jul 5;49(4):303–311. doi: 10.1111/age.12677

Table 2.

Animal‐wise imputation accuracy by scenario

Scenario Proportion of correctly imputed genotypes (% correct)a Correlation between true and imputed genotypes (corr)a
Average SD Average SD
Ref90b 98.626 1.677 0.948 0.078
REf90NoPedb 98.553 1.674 0.946 0.078
Ref50b 98.390 1.819 0.939 0.088
Ref50NoPedb 98.315 1.817 0.938 0.088
Ref10b 97.432 2.359 0.916 0.095
Ref10NoPedb 97.373 2.351 0.915 0.095
RELc 98.792 1.213 0.972 0.035
REL‐Cc 97.668 2.265 0.926 0.086
a

Statistics were calculated across all 10 replicates for the particular scenarios except for REL, for which there were no replicates.

b

Dogs were randomly grouped into the reference and the validation sets, and 87.5% of genotypes were masked in the high‐density array to generate the low‐density array; Ref90, 90% of dogs in the reference set; Ref50, 50% of dogs in the reference set; Ref10, 10% of dogs in the reference set; NoPed, indicates that the imputation of the particular variant was run without pedigree information.

c

Dogs in the reference set (31%) had at least one half‐sibling in the validation set (REL; 69%). The REL‐C controls had the same number of dogs as REL, but dogs were selected at random for the reference and the validation sets. In REL and REL‐C, 87.5% of genotypes were also masked in the high‐density array to generate the low‐density array.