Status
Assembly v1 (October 2015) is a standard draft assembly of PacBio and Illumina gDNA reads. A total of 405 scaffolds and 44.8 Mbp were assembled with Falcon, improved with finisherSC, and polished with Quiver.
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 Caloscypha fulgens v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 44.84 |
| Sequencing read coverage depth | |
| # of contigs | 405 |
| # of scaffolds | 405 |
| # of scaffolds >= 2Kbp | 403 |
| Scaffold N50 | 56 |
| Scaffold L50 (Mbp) | 0.24 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 0.76, 0.70, 0.69 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 62836 | 57486 | 91.5% |
| Ests | est.fasta | 170569950 | 162095165 | 95.0% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1760 | 1497 |
| transcript | 1472 | 1225 |
| exon | 367 | 235 |
| intron | 98 | 75 |
| description: | ||
| protein length (aa) | 420 | 331 |
| exons per gene | 4.01 | 3 |
| # of gene models | 9203 |
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.
