Status
Assembly v1 (Jul 2014) is an improved draft assembly. A total of 2516 scaffolds and 89.1 Mbp were assembled from Illumina gDNAs using AllPathsLG and improved with PacBio reads and PBJelly.
Summary statistics for the Gymnopus androsaceus JB14 v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 89.15 |
| Sequencing read coverage depth | ??x |
| # of contigs | 2519 |
| # of scaffolds | 2516 |
| # of scaffolds >= 2Kbp | 1776 |
| Scaffold N50 | 144 |
| Scaffold L50 (Mbp) | 0.17 |
| # of gaps | 3 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 1.23, 1.07, 1.01 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | JGI_RNA_contigs | 53709 | 51188 | 95.3% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1479 | 1193 |
| transcript | 1143 | 932 |
| exon | 211 | 135 |
| intron | 78 | 57 |
| description: | ||
| protein length (aa) | 341 | 266 |
| exons per gene | 5.43 | 4 |
| # of gene models | 29375 |
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
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.
