Table 4 Difference between concordance using PLINK clustering for one or two steps of imputation (directly from low density or low to medium to high) compared to using all animals in the reference population per breed and proportion of animals with improved accuracy for different imputation reference populations
Breed | PLINK (1 step) average change in accuracy after clustering | PLINK (1 step) Proportion of individuals in group with improved accuracy | PLINK (2 steps) average change in accuracy after clustering | PLINK (2 steps) Proportion of individuals in group with improved accuracy |
|---|---|---|---|---|
Alberta Composite | 0.035 | 0.714 | 0.004 | 0.714 |
Angus | 0.005 | 0.727 | 0.004 | 0.727 |
Red Angus | 0.000 | 0.000 | 0.00 | 0.400 |
Ayrshire | −0.001 | 0.800 | −0.002 | 1.000 |
BeefBooster | 0.005 | 0.000 | 0.022 | 0.000 |
Brown Swiss | 0.021 | 0.917 | 0.020 | 0.917 |
Charolais | 0.060 | 0.500 | 0.062 | 0.000 |
Gelbvieh | 0.001 | 1.000 | 0.044 | 1.000 |
Guelph Composite | 0.000 | 0.200 | 0.003 | 0.200 |
Hereford | 0.000 | 0.429 | 0.002 | 0.286 |
Holstein | −0.007 | 0.500 | −0.005 | 0.362 |
Red and White Holstein | 0.001 | 0.250 | 0.005 | 0.000 |
Jersey | −0.014 | 0.833 | −0.016 | 1.000 |
Limousin | 0.054 | 0.667 | 0.063 | 0.500 |
Montbeliarde | −0.012 | 0.833 | −0.003 | 1.000 |
Normande | −0.001 | 1.000 | −0.002 | 1.000 |
Simmental | −0.028 | 0.500 | −0.026 | 0.568 |