Table 2.
Overall and subgenome assessment of homoeolog expression estimation
| GSNAP-PolyCat | HyLiTE | EAGLE-RC | RSEM | Salmon | Kallisto | Bowtie2 | ||
|---|---|---|---|---|---|---|---|---|
| Reference | D 5 | D 5 | A 2 | A 2 and D 5 | Polyploid AD | |||
| Efficiency | 87.7 ± 1.5% | 82.2 ± 0.7% | 81.5 ± 0.7% | 96.3 ± 0.8% | 100.0% | 100.0% | 100.0% | 84.9 ± 1.5% |
| At | 86.7 ± 1.6% | 78.5 ± 1.0% | 82.7 ± 0.7% | 95.5 ± 0.9% | 101.0 ± 0.6% | 101.6 ± 0.5% | 101.5 ± 0.6% | 84.6 ± 1.5% |
| Dt | 88.6 ± 1.6% | 85.8 ± 0.6% | 80.3 ± 0.9% | 97.1 ± 1.0% | 99.1 ± 0.6% | 98.5 ± 0.5% | 98.6 ± 0.6% | 85.1 ± 1.6% |
| Discrepancy | 12.7 ± 1.5% | 18.1 ± 0.8% | 18.7 ± 0.8% | 5.1 ± 0.8% | 5.1 ± 0.6% | 5.1 ± 0.6% | 5.1 ± 0.6% | 15.9 ± 1.5% |
| At | 13.4 ± 1.6% | 21.0 ± 1.1% | 17.5 ± 0.8% | 5.4 ± 0.9% | 5.4 ± 0.6% | 5.2 ± 0.6% | 5.2 ± 0.6% | 16.0 ± 1.5% |
| Dt | 12.1 ± 1.5% | 14.8 ± 0.6% | 20.0 ± 0.9% | 4.8 ± 0.8% | 4.8 ± 0.6% | 5.1 ± 0.6% | 5.0 ± 0.6% | 15.7 ± 1.5% |
| Precision | – | – | – | – | – | – | – | – |
| At | 98.4 ± 0.1% | 92.4 ± 0.3% | 91.9 ± 0.4% | 98.1 ± 0.1% | 95.1 ± 0.2% | 94.3 ± 0.2% | 94.4 ± 0.2% | 95.5 ± 0.1% |
| Dt | 97.7 ± 0.5% | 91.2 ± 0.6% | 91.6 ± 0.5% | 97.2 ± 0.5% | 97.0 ± 0.5% | 96.5 ± 0.4% | 96.4 ± 0.4% | 96.1 ± 0.5% |
| Recall | – | – | – | – | – | – | – | – |
| At | 97.7 ± 0.5% | 90.6 ± 0.6% | 93.1 ± 0.4% | 97.2 ± 0.4% | 96.5 ± 0.5% | 96.4 ± 0.4% | 96.4 ± 0.4% | 96.4 ± 0.5% |
| Dt | 98.1 ± 0.1% | 94.0 ± 0.3% | 91.3 ± 0.4% | 97.9 ± 0.1% | 96.2 ± 0.2% | 95.4 ± 0.2% | 95.4 ± 0.2% | 95.0 ± 0.1% |
| F 1 score | – | – | – | – | – | – | – | – |
| At | 98.7 ± 0.2% | 92.2 ± 0.4% | 92.9 ± 0.3% | 98.1 ± 0.2% | 97.2 ± 0.3% | 96.8 ± 0.2% | 96.9 ± 0.2% | 97.0 ± 0.3% |
| Dt | 98.7 ± 0.2% | 93.1 ± 0.4% | 92.1 ± 0.3% | 98.0 ± 0.2% | 97.2 ± 0.3% | 96.7 ± 0.2% | 96.7 ± 0.2% | 96.9 ± 0.3% |
| Accuracy* | 98.2 ± 0.2% | 93.7 ± 0.7% | 93.6 ± 0.3% | 97.7 ± 0.2% | 96.3 ± 0.3% | 95.7 ± 0.2% | 95.8 ± 0.2% | 96.2 ± 0.2% |
| MCC* | 96.8 ± 0.5% | 84.5 ± 0.7% | 84.2 ± 0.7% | 95.8 ± 0.4% | 95.5 ± 0.5% | 94.7 ± 0.4% | 94.8 ± 0.4% | 94.2 ± 0.5% |
Note: The best performance for each metric is marked in bold text.
*Same values for At and Dt reads.