Status
Assembly v1 (April 2015) is a standard draft assembly of Illumina gDNA reads. A total of 68 scaffolds and 46.1 Mbp were assembled with AllPathsLG.
Annotation v1 (April 2016) is a standard draft annotation using RNA-Seq, contigs assembled thereof by Trinity, and the JGI Annotation Pipeline.
Summary statistics for the Khuskia oryzae ATCC 28132 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 46.05 |
| Sequencing read coverage depth | 94.9x |
| # of contigs | 701 |
| # of scaffolds | 68 |
| # of scaffolds >= 2Kbp | 56 |
| Scaffold N50 | 6 |
| Scaffold L50 (Mbp) | 3.41 |
| # of gaps | 633 |
| % of scaffold length in gaps | 1.3% |
| Three largest Scaffolds (Mbp) | 4.83, 4.31, 4.18 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 45204 | 43318 | 95.8% |
| Ests | est.fasta | 135347860 | 128483327 | 94.9% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 1644 | 1394 |
| transcript | 1467 | 1230 |
| exon | 569 | 360 |
| intron | 114 | 71 |
| description: | ||
| protein length (aa) | 419 | 336 |
| exons per gene | 2.58 | 2 |
| # of gene models | 13375 |
Collaborators
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.
