Status
Assembly v1 (April 2013) is a standard draft assembly of Solexa gDNA reads. A total of 54 scaffolds and 52.4 Mbp were assembled using AllPathsLG.
Summary statistics for the Chalara longipes BDJ v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 52.43 |
| Sequencing read coverage depth | 104.7x |
| # of contigs | 175 |
| # of scaffolds | 54 |
| # of scaffolds >= 2Kbp | 41 |
| Scaffold N50 | 9 |
| Scaffold L50 (Mbp) | 2.69 |
| # of gaps | 121 |
| % of scaffold length in gaps | 0.3% |
| Three largest Scaffolds (Mbp) | 3.39, 3.26, 3.22 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | JGI_Rnnotator_RNA_contigs | 47759 | 44984 | 94.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1646 | 1418 |
| transcript | 1483 | 1269 |
| exon | 485 | 306 |
| intron | 81 | 56 |
| description: | ||
| protein length (aa) | 442 | 368 |
| exons per gene | 3.06 | 3 |
| # of gene models | 19765 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Barbi F, Kohler A, Barry K, Baskaran P, Daum C, Fauchery L, Ihrmark K, Kuo A, LaButti K, Lipzen A, Morin E, Grigoriev IV, Henrissat B, Lindahl BD, Martin F
Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers.
Environ Microbiol. 2020 Mar;22(3):1089-1103. doi: 10.1111/1462-2920.14873
Barbi F, Kohler A, Barry K, Baskaran P, Daum C, Fauchery L, Ihrmark K, Kuo A, LaButti K, Lipzen A, Morin E, Grigoriev IV, Henrissat B, Lindahl BD, Martin F
Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers.
Environ Microbiol. 2020 Mar;22(3):1089-1103. doi: 10.1111/1462-2920.14873
Links
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.
