Table 1.
Comparison of Meug genome assemblies
| Assembly version | |||
|---|---|---|---|
| 1.0 | 1.1 | 2.0 | |
| Contigs (million) | 1.211 | 1.174 | 1.111 |
| N50 (kb) | 2.5 | 2.6 | 2.91 |
| Bases (Mb) | 2546 | 2,536 | 2,574 |
| Scaffolds | 616,418 | 277,711 | 379,858 |
| Max scaffold size | NA | 472,108 | 324,751 |
| Gaps (Mb) | NA | 539 | 619 |
| N50 (kb) | NA | 41.8 | 34.3 |
| Complex scaffolds | NA | 128,563 | 124,674 |
| Singleton scaffolds | NA | 149,148 | 255,184 |
| Co-linear with BACs | NA | 87.2% (418) | 93.4% (298) |
| Co-linear with ESTs | NA | 82.3% (704) | 86.7% (454) |
Summary statistics for the tammar genome assemblies. These statistics indicate the extension and merging of contigs done to improve the assembly. The larger number of scaffolds and smaller scaffold N50 is a consequence of higher stringency in the 2.0 scaffolding workflow. The higher stringency isolated many contigs. However, the number of complex (that is, useful) scaffolds is similar between the assemblies. For co-linear estimates, the scaffolds were linearized and BACs and cDNA libraries were mapped against them. The 1.1 and 2.0 assemblies were validated against 169 BAC contigs and 84,718 ESTs (that were not incorporated into either genome assembly). We determined the percentage of contigs where the scaffolding matched the order and orientation when compared to BACs or ESTs (co-linear with BACs/ESTs). Parentheses indicate the total number of contigs identified after alignment to BAC contigs or ESTs.