Status
Assembly v1.0 (January 2011) is a draft assembly of 454 gDNA reads and shredded Velvet contigs. The latter were assembled from Solexa gDNA reads. A total of 39 scaffolds and 31.9 Mbp were assembled using Newbler.
Annotation v1.1 (October 2014) is a draft annotation using RNASeq data available September 2014.
Summary statistics for the Xanthoria parietina 46-1-SA22
v1.1 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 31.90 |
| Sequencing read coverage depth | 43.84x |
| # of contigs | 302 |
| # of scaffolds | 39 |
| # of scaffolds >= 2Kbp | 39 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 1.73 |
| # of gaps | 263 |
| % of scaffold length in gaps | 0.3% |
| Three largest Scaffolds (Mbp) | 3.93, 2.80, 2.31 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | JGI_lichen_RNA_contigs | 239449 | 34663 | 14.5% |
| Other | JGI_mycobiont_RNA_contigs | 27817 | 26125 | 93.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1691 | 1437 |
| transcript | 1529 | 1269 |
| exon | 510 | 302 |
| intron | 83 | 59 |
| description: | ||
| protein length (aa) | 434 | 342 |
| exons per gene | 3.00 | 3 |
| # of gene models | 11065 |
Collaborators
- DOE Joint Genome Institute
- Paul Dyer at U of Nottingham.
- Peter Crittenden at U of Nottingham.
- David Archer at U of Nottingham.
Funding
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.
