Status
[September 2017] [Aug 2017] The Setosphaeria turcica genome was
sequenced using the Illumina platform and assembled with AllPathsLG
release version R49403 (Gnerre
et al., 2010) in July 2015. This is an updated annotation of
the same assembly using RNA-seq reads from
various growth conditions to improve gene calling.
Mitochondrial genome was assembled separately and is available in
the downloads section.
Summary statistics for the Setosphaeria turcica NY001 v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 38.42 |
| Sequencing read coverage depth | 58.1x |
| # of contigs | 1823 |
| # of scaffolds | 489 |
| # of scaffolds >= 2Kbp | 417 |
| Scaffold N50 | 45 |
| Scaffold L50 (Mbp) | 0.23 |
| # of gaps | 1334 |
| % of scaffold length in gaps | 6.0% |
| Three largest Scaffolds (Mbp) | 1.75, 1.20, 0.88 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 34363 | 31396 | 91.4% |
| Ests | est.fasta | 472709595 | 167488904 | 35.4% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1625 | 1373 |
| transcript | 1496 | 1254 |
| exon | 581 | 364 |
| intron | 84 | 58 |
| description: | ||
| protein length (aa) | 439 | 355 |
| exons per gene | 2.58 | 2 |
| # of gene models | 12547 |
Collaborators
Gillian Turgeon, Cornell University
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.
