Status
Assembly v1 (May 2015) is a standard draft assembly of Illumina gDNA reads using AllPathsLG.
Annotation v1 (April 2016) is a standard draft annotation using RNA-Seq, contigs assembled thereof by Trinity, and the JGI Annotation Pipeline.
61% of the RNA-Seq reads were rRNA, accounting for the 46% rate of mapping of the reads on the Illumina-sequenced genomic assembly.
Summary statistics for the Plectania melastoma v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 92.51 |
| Sequencing read coverage depth | 72.3x |
| # of contigs | 504 |
| # of scaffolds | 175 |
| # of scaffolds >= 2Kbp | 157 |
| Scaffold N50 | 23 |
| Scaffold L50 (Mbp) | 1.36 |
| # of gaps | 329 |
| % of scaffold length in gaps | 0.5% |
| Three largest Scaffolds (Mbp) | 3.55, 3.10, 2.93 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 48648 | 46978 | 96.6% |
| Ests | est.fasta | 121594175 | 55623149 | 45.7% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1587 | 1333 |
| transcript | 1367 | 1116 |
| exon | 382 | 242 |
| intron | 87 | 60 |
| description: | ||
| protein length (aa) | 399 | 314 |
| exons per gene | 3.58 | 3 |
| # of gene models | 16180 |
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.
