Table 1 Measures of imputation success for single- and mixed-density data by age group
Markers used | Â | 50 K | Mixed | Mixed | 500 K |
|---|---|---|---|---|---|
Number of 500 K genotypes | Â | 0 | 1,406 | 3,798 | 33,414 |
| Â | Age1: | Â | Â | Â | Â |
Missing before imputation (%) | all | 1 | 86 | 80 | 1 |
Missing after imputation (%) | all | 0.04 | 6.4 | 3.3 | 0.05 |
Genotype error rate (%) | young | 0.03 | 1.3 | 0.9 | 0.03 |
| Â | old | 0.04 | 3.4 | 1.7 | 0.04 |
Incorrect genotypes (%) | young | 0.06 | 2.6 | 1.7 | 0.06 |
| Â | old | 0.08 | 7.3 | 3.4 | 0.08 |
Incorrect linkage phase (%) | young | 0.3 | 1.9 | 1.4 | 0.1 |
| Â | old | 0.4 | 5.4 | 2.5 | 0.2 |
Incorrect paternity (%) | young | 2.0 | 4.9 | 5.0 | 2.5 |
| Â | old | 4.3 | 7.6 | 6.2 | 4.2 |
Correlation2 (estimated, true genotypes) | all | 0.99 | 0.84 | 0.93 | 0.99 |
Reliability of linear breeding values (%) | young | 82.6 | 83.4 | 83.7 | 84.1 |
Reliability of nonlinear breeding values (%) | young | 84.4 | 85.3 | 85.6 | 86.0 |
Reliability gain (nonlinear), 500 K - 50 K (%) | young | 0.0 | 0.9 | 1.2 | 1.6 |