Info • Cladonia grayi Cgr/DA2myc/ss v1.0
Assembly v1 (28 July 2010) is a draft assembly of 454 gDNA reads and shredded Velvet contigs. The latter were assembled from Solexa gDNA reads. A total of 1506 scaffolds and 39.6 Mbp were assembled using Newbler:
| Nuclear Genome Assembly: | v1.0 |
| Scaffold count: | 1506 |
| All Contig count: | 5214 |
| Scaffold sequence bases total: | 39.6 Mbp |
| Scaffolded (Large) Contig sequence bases total: | 38.4 Mbp |
| Estimated % sequence bases in gaps: | 3.0% |
| Scaffold N50 / L50: | 45 / 219.1 kbp |
| Contig N50 / L50: | 342 / 14.9 kbp |
| Number of scaffolds > 50.0 Kb: | 140 |
| % in scaffolds > 50.0 Kb: | 77.6% |
| % assembly masked by repeats: | 7.2% |
| # ESTs: | 740680 |
| % ESTs that align with assembly: | 65% |
Annotation v1 (28 July 2010) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of cDNA-based, protein-based, and ab initio gene predictors. After filtering for EST and protein homology support, a total of 11415 genes were structurally and functionally annotated.
| Nuclear Genome Annotation: | v1.0 |
| # gene models: | 11415 |
| Gene density: | 288 genes per Mbp scaffold |
| Avg.gene length: | 1832 nt |
| Avg. protein length: | 441 aa |
| Avg. exon frequency: | 3.25 exons per gene |
| % genes with intron: | 81 % |
| % complete gene models (with start and stop codons): | 83% |
| % genes with NR support: | 87% |
| % genes with Pfam domains: | 53% |
| % genes with transmembrane domain: | 19% |
| % genes in multigene family: | 60% |
| % genes with EST support: | 83% |
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
