Status
(Aug 2016) The Panellus stipticus LUM genome was sequenced using PacBio RS Regular (DNA) 1 x 240 bp 8.93 kb. Each fastq file was QC filtered with smrtanalysis and subsequently assembled with Falcon, improved with finisherSC, and polished with Quiver to produce an assembly with 379 scaffolds.
The JGI annotation pipeline identified 7,089 gene models as possible diploid alleles, and excluded them from the filtered model/gene catalog set. These models are shown in the track "secondary_alleles", and are available from the download page.
Summary statistics for the Panellus stipticus LUM v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 57.18 |
| Sequencing read coverage depth | 157.6x |
| # of contigs | 379 |
| # of scaffolds | 379 |
| # of scaffolds >= 2Kbp | 379 |
| Scaffold N50 | 32 |
| Scaffold L50 (Mbp) | 0.39 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 2.19, 2.14, 2.13 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 168296397 | 166643121 | 99.0% |
| Other | JGI_RNA_contigs | 66231 | 64346 | 97.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1632 | 1361 |
| transcript | 1316 | 1101 |
| exon | 218 | 136 |
| intron | 65 | 54 |
| description: | ||
| protein length (aa) | 387 | 312 |
| exons per gene | 6.05 | 5 |
| # of gene models | 16771 |
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.
