Status
[September 2016] The Rhodosporidum toruloides IFO0880 genomes was sequenced externally in the lab of Dr. Jeffrey Skerker using PacBio, assembled with HGAP, then annotated with the JGI annotation pipeline.
Summary statistics for the Rhodosporidium toruloides
IFO0880 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 20.81 |
| Sequencing read coverage depth | |
| # of contigs | 30 |
| # of scaffolds | 30 |
| # of scaffolds >= 2Kbp | 30 |
| Scaffold N50 | 6 |
| Scaffold L50 (Mbp) | 1.39 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 2.22, 1.97, 1.86 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 257698825 | 255851744 | 99.3% |
| Ests | RNNotator_assembled_Illumina_ESTs | 31376 | 30219 | 96.3% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 2160 | 1809 |
| transcript | 1746 | 1446 |
| exon | 281 | 170 |
| intron | 81 | 64 |
| description: | ||
| protein length (aa) | 518 | 412 |
| exons per gene | 6.21 | 5 |
| # of gene models | 8232 |
Collaborators
John
Gladden, Joint Bioenergy Institute (JBEI)
Jeffrey
Skerker, UC Berkeley
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.
