Table 3.
Error rates found by each method when using cut-offs for the probabilities provided by PHASE
| GH1 – cutoff 70% (5 SNPs) | ||||
| MD | Method | Abs IER | Rel IER | Res rate |
| 0% | Global | 2.18% | 2.24% | 97.31% |
| Local | 2.56% | 2.65% | 96.54% | |
| 2% | Global | 2.92% | 2.99% | 96.78% |
| Local | 2.97% | 3.05% | 94.78% | |
| 5% | Global | 3.33% | 3.49% | 95.38% |
| Local | 3.17% | 3.51% | 90.42% | |
| 10% | Global | 4.50% | 4.92% | 91.40% |
| Local | 4.07% | 5.00% | 81.50% | |
| 15% | Global | 5.83% | 6.56% | 88.88% |
| Local | 4.85% | 6.42% | 75.54% | |
| 20% | Global | 7.06% | 8.14% | 86.80% |
| Local | 6.00% | 8.81% | 68.12% | |
| GH1 – cutoff 50% (5 SNPs) | ||||
| MD | Method | Abs IER | Rel IER | Res rate |
| 0% | Global | 2.99% | 2.99% | 99.82% |
| Local | 3.50% | 3.50% | 99.83% | |
| 2% | Global | 3.82% | 3.98% | 99.81% |
| Local | 4.18% | 4.26% | 97.47% | |
| 5% | Global | 5.03% | 5.06% | 99.42% |
| Local | 5.08% | 5.32% | 95.45% | |
| 10% | Global | 7.17% | 7.28% | 98.45% |
| Local | 7.24% | 8.04% | 90.06% | |
| 15% | Global | 9.41% | 9.62% | 97.84% |
| Local | 9.50% | 10.95% | 86.83% | |
| 20% | Global | 11.25% | 11.58% | 97.18% |
| Local | 11.96% | 14.45% | 82.77% | |
This table presents the summary of average error rates when using a cut-off on resolution probability given by PHASE instead of Rmax when choosing the resolution obtained by each method. The 2 cut-offs chosen were respectively 50% and 70%. The error rate is almost always lower than with Rmax, but the number of assigned haplotypes strongly decreased.
IER: individual error rate, Abs IER: absolute IER, Rel IER: relative IER, Res Rate: resolution rate, MD: Missing Data.