Table 1. Simulation results averaged across 1000 replicates of eight-parent MAGIC populations.
M | N | %MISS | %F0 | %F | %FC | %FK | %K | %B | %M |
---|---|---|---|---|---|---|---|---|---|
101 | 200 | 30 | 46.9 | 100 | 100 | 86.6 | 79.8 | 93.7 | 96.3 |
101 | 200 | 40 | 24.5 | 100 | 100 | 85.4 | 78.8 | 93.0 | 95.5 |
101 | 200 | 50 | 9.8 | 100 | 99.6 | 83.9 | 77.5 | 92.0 | 94.8 |
101 | 200 | 60 | 3.5 | 99.9 | 98.3 | 81.6 | 75.7 | 88.7 | 93.2 |
101 | 400 | 30 | 47.3 | 100 | 100 | 88.4 | 80.3 | 94.3 | 96.3 |
101 | 400 | 40 | 24.9 | 100 | 100 | 87.4 | 79.4 | 93.8 | 95.5 |
101 | 400 | 50 | 10.1 | 100 | 100 | 86.2 | 78.2 | 92.6 | 94.8 |
101 | 400 | 60 | 3.6 | 100 | 99.7 | 84.3 | 76.7 | 90.7 | 93.5 |
201 | 200 | 30 | 47.1 | 100 | 100 | 90.7 | 83.5 | 96.7 | 98.3 |
201 | 200 | 40 | 24.8 | 100 | 100 | 89.5 | 82.3 | 96.3 | 98.0 |
201 | 200 | 50 | 10.0 | 100 | 100 | 87.8 | 80.8 | 95.4 | 97.6 |
201 | 200 | 60 | 2.9 | 100 | 99.7 | 85.2 | 78.8 | 91.2 | 96.8 |
201 | 400 | 30 | 47.1 | 100 | 100 | 92.1 | 84.1 | 97.0 | 98.3 |
201 | 400 | 40 | 24.9 | 100 | 100 | 91.3 | 83.1 | 96.5 | 98.0 |
201 | 400 | 50 | 10.0 | 100 | 100 | 90.1 | 81.8 | 96.0 | 97.6 |
201 | 400 | 60 | 2.8 | 100 | 100 | 88.2 | 80.0 | 94.3 | 96.8 |
For each scenario we record the percent of markers with complete founder genotypes originally (%F0), the percentage complete after imputation (%F), the percentage of missing founder genotypes correctly imputed (%FC), the percentage correctly imputed based on the five nearest neighbor markers (%FK), the percentage of missing progeny genotypes correctly imputed based on the five nearest neighbor markers (%K), the percentage correctly imputed with BEAGLE (%B), and the percentage correctly imputed with R/mpMap (%M).