Status
Assembly v1 (October 2011) is a draft assembly of Sanger and 454 genomic reads. A total of 4890 scaffolds and 218.7 Mbp were assembled using Arachne.
Summary statistics for the Pseudo-nitzschia multiseries
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 218.73 |
| Sequencing read coverage depth | 8.79x |
| # of contigs | 20216 |
| # of scaffolds | 4890 |
| # of scaffolds >= 2Kbp | 4828 |
| Scaffold N50 | 390 |
| Scaffold L50 (Mbp) | 0.15 |
| # of gaps | 15326 |
| % of scaffold length in gaps | 8.5% |
| Three largest Scaffolds (Mbp) | 1.17, 0.96, 0.86 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | nutrient replete ESTs | 21731 | 19413 | 89.3% |
| Ests | pooled ESTs: temp shock, senescence, L/D cycle, P- | 30633 | 28066 | 91.6% |
| Ests | pooled ESTs: Si- and Fe- | 22180 | 14975 | 67.5% |
| Other | EST_cluster_consensi | 16535 | 11995 | 72.5% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1522 | 1163 |
| transcript | 1209 | 978 |
| exon | 509 | 315 |
| intron | 229 | 110 |
| description: | ||
| protein length (aa) | 377 | 298 |
| exons per gene | 2.38 | 2 |
| # of gene models | 19703 |
Collaborators
- DOE Joint Genome Institute
- E. Virginia Armbrust at U. Washington
- Micaela S. Parker at U. Washington
- Gabrielle Rocap at U. Washington
- Bethany Jenkins at U. Rhode Island
- Stephen S. Bates at Fisheries and Oceans Canada
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.
