Table 4.
Comparison of Average Completeness of Recovered Coding Regions Obtained Using Different Assemblers
| Species | Average Completeness (%) |
|||||
|---|---|---|---|---|---|---|
| BWA (Default) | BWA (b = 2) | NGM | STAMPY | STAMPY (Div. = 0.1) | BT2 | |
| Anole (control) | 94.1 | 94.8 | 91.9 | 89.8 | — | 74.1 |
| Leopard lizard | 84.9 | 88.2 | 89.5 | 91.1 | — | 37.4 |
| Chameleon | 63.4 | 72.8 | 81.5 | 85.7 | — | 42.0 |
| Monitor | 70.3 | 77.7 | 83.9 | 88.8 | — | 38.2 |
| Glossy snake | 54.7 | 64.4 | 74.3 | 86.5 | — | 28.3 |
| Scarlet snake | 59.2 | 67.8 | 75.2 | 87.1 | — | 32.0 |
| King snake | 54.6 | 64.8 | 73.4 | 86.7 | — | 32.0 |
| Corn snake | 53.9 | 62.6 | 72.3 | 85.5 | — | 26.5 |
| Leaf-nosed sn. | 60.3 | 67.6 | 77.0 | 87.3 | — | 21.8 |
| Long-nosed sn. | 53.2 | 61.5 | 73.0 | 86.4 | — | 31.1 |
| Night snake | 54.4 | 64.2 | 72.8 | 86.4 | — | 27.5 |
| Garter snake | 53.8 | 63.8 | 73.2 | 85.9 | — | 31.0 |
| Plated lizard | 65.7 | 75.2 | 81.8 | 86.7 | — | 37.2 |
| Tokay gecko | 59.2 | 69.4 | 79.6 | 85.4 | 85.3 | 47.6 |
| Giant day gecko | 60.0 | 69.1 | 78.2 | 84.5 | 84.2 | 43.9 |
| Reef gecko | 55.4 | 65.6 | 77.3 | 84.3 | 84.0 | 42.3 |
| AVERAGE | 62.3 | 70.6 | 78.4 | 86.8 | 84.5 | 37.1 |
Note.––All assembly was done to the Anolis reference. Abbreviations—Div., divergence parameter; BT2, Bowtie 2.