Status
December 2011, version 1.0. This draft assembly was produced using Roche (454) and shredded consensus from Velvet-assembled Illumina data.
Summary statistics for the Acidomyces richmondensis BFW
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 29.88 |
| Sequencing read coverage depth | 17.1x |
| # of contigs | 3164 |
| # of scaffolds | 3164 |
| # of scaffolds >= 2Kbp | 1580 |
| Scaffold N50 | 191 |
| Scaffold L50 (Mbp) | 0.04 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 0.22, 0.19, 0.19 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | ESTs (RNAseq data assembled using RNNotator) | 37087 | 28488 | 76.8% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1485 | 1270 |
| transcript | 1375 | 1156 |
| exon | 602 | 342 |
| intron | 88 | 63 |
| description: | ||
| protein length (aa) | 405 | 333 |
| exons per gene | 2.28 | 2 |
| # of gene models | 11202 |
Collaborators
- Steven Singer, DOE JBEI, Berkeley, CA
- Igor Grigoriev, DOE JGI, Walnut Creek, CA
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.
Front Microbiol. 2016;7():238. doi: 10.3389/fmicb.2016.00238
Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.
Front Microbiol. 2016;7():238. doi: 10.3389/fmicb.2016.00238
Links
- Acidomyces richmondensis, assembly of metagenomic sample
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.
