Table 1 Summary metrics of the four assemblies showing the relative levels of completeness and fragmentation
From: Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes
| Â | A. halleri halleri | A. halleri gemmifera | A.lyrata | A. thaliana |
|---|---|---|---|---|
Nb scaffolds | 3152 | 2239 | 695 | 7 |
Total length | 174 Mb | 196 Mb | 207 Mb | 120 Mb |
Genome cov. | 68.3% | 76.9% | 89.9% | 88.9% |
Longest scaff. | 1.5 Mb | 4.3 Mb | 33.1 Mb | 30.4 Mb |
N50 | 279,389 | 712,249 | 24,464,547 | 23,459,830 |
L50 | 177 | 71 | 4 | 3 |
CDS content | 18.7% | 19.5% | 16.3% | 35.4% |
non-CDS gene content | 19.3% | 19.6% | 15.9% | 14.9% |
Number of TEs | 68,583 | 85,835 | 87,477 | 39,210 |
TE content (TE content estimation) | 15.2% (32.7%) | 20.8% (30.2%) | 27.8% (24.5%) | 17.4% (19.1%) |
Other repeats content | 4.5% | 5.4% | 5.8% | 4.3% |
Unannotated bases | 42.2% | 34.8% | 34.7% | 28.1% |
Complete universal single-copy orthologs | 95.3% | 97.6% | 98.5% | 98.2% |
Fragmented universal single-copy orthologs | 1.5% | 0.3% | 0.3% | 0.5% |
Missing universal single-copy orthologs | 3.2% | 2.1% | 1.2% | 1.3% |