Table 3.
Median imputation accuracy for non-sequenced individuals as a function of used sequencing datasets and individual’s SNP array genotype status for (a) all non-sequenced individuals or (b) the final four quintiles of the population
| High density | Low density | No genotype | |
|---|---|---|---|
| (a) All individuals | |||
| Focal | 0.967 | 0.936 | 0.855 |
| Focal and low coverage sires | 0.983 | 0.952 | 0.863 |
| Focal and all low coverage (all sequenced) | 0.987 | 0.971 | 0.881 |
| findhap with all sequenced | 0.958 | 0.892 | 0.702 |
| (b) Final four quintiles | |||
| Focal | 0.968 | 0.968 | 0.939 |
| Focal and low coverage sires | 0.984 | 0.985 | 0.953 |
| Focal and all low coverage (all sequenced) | 0.987 | 0.988 | 0.959 |
| findhap with all sequenced | 0.959 | 0.916 | 0.765 |