Table 5.
EMD from predicted haplotypes to the true haplotype population for 1K-, 2K-, 5K-long and full-length genomic regions for HIV, HCV and ZIKV benchmarks
| CliqueSNV | |||||||
|---|---|---|---|---|---|---|---|
| Benchmark | Length | Consensus | 2% | 5% | 10% | PredictHaplo | aBayesQR |
| HCV10sim | 1K | 1.109 | 0.080 | 0.037 | 0.143 | 1.479 | did not finish |
| 2K | 3.397 | 0.714 | 0.854 | 1.923 | 0.981 | did not finish | |
| 5K | 3.719 | 3.729 | 3.729 | 1.431 | 0.450 | did not finish | |
| full-length | 3.335 | 3.335 | 3.335 | 1.217 | 0.140 | did not finish | |
| ZIKV3sim | 1K | 2.408 | 0.015 | 0.015 | 0.015 | 0.100 | 0.086 |
| 2K | 2.388 | 0.020 | 0.020 | 0.020 | 0.092 | did not finish | |
| 5K | 2.182 | 0.010 | 0.010 | 0.010 | 0.031 | did not finish | |
| full-length | 2.168 | 0.007 | 0.007 | 0.007 | 0.016 | did not finish | |
| ZIKV15sim | 1K | 3.368 | 1.123 | 1.335 | 1.840 | 3.640 | 1.345 |
| 2K | 3.571 | 1.469 | 1.339 | 3.128 | 7.037 | 1.807 | |
| 5K | 3.506 | 1.379 | 1.778 | 1.698 | 6.701 | did not finish | |
| full-length | 3.803 | 1.254 | 1.643 | 2.801 | 6.014 | did not finish | |
| HIV5full | 1K | 1.480 | 0.696 | 0.350 | 0.590 | 0.943 | 1.405 |
| 2K | 3.460 | 2.081 | 2.100 | 2.626 | 2.825 | 3.100 | |
| 5K | 2.384 | 2.219 | 1.500 | 1.997 | 2.267 | did not finish | |
| full-length | 3.189 | 2.968 | 2.557 | 2.273 | 1.811 | did not finish | |
| Average over all benchmarks | 2.957 | 1.401 | 1.371 | 1.438 | 2.203 | 1.548* | |
The EMD is normalized by the genomic region length, i.e. we report the EMD per 100 genomic positions. Comparison is performed for Clique-SNV with three different frequency thresholds: 2, 5 (default) and 10%, aBayesQR and PredictHaplo . The aBayesQR did not finish in majority of samples. The best EMD for each benchmark is in bold font.