Status
[March 2018] Assembly v1 is a draft assembly extracted from a lichen metagenome by aligning the reads with the reference mycobiont genome. The aligned Illumina gDNAs were assembled with Velvet and then AllPathsLG. The mitochondrial assembly is available in the Download page.
Annotation v1 is a draft annotation, using RNASeq reads aligned with the extracted mycobiont genome and then assembled with Trinity. Genes were modeled with the JGI Annotation Pipeline v1.10
Summary statistics for the Lobaria pulmonaria Africa v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 55.03 |
| Sequencing read coverage depth | 143.4x |
| # of contigs | 1952 |
| # of scaffolds | 1556 |
| # of scaffolds >= 2Kbp | 1556 |
| Scaffold N50 | 266 |
| Scaffold L50 (Mbp) | 0.06 |
| # of gaps | 396 |
| % of scaffold length in gaps | 0.4% |
| Three largest Scaffolds (Mbp) | 0.59, 0.41, 0.40 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 171808100 | 170559964 | 99.3% |
| Other | JGI_RNA_contigs | 76908 | 70551 | 91.7% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1544 | 1310 |
| transcript | 1383 | 1144 |
| exon | 471 | 291 |
| intron | 85 | 60 |
| description: | ||
| protein length (aa) | 396 | 309 |
| exons per gene | 2.94 | 2 |
| # of gene models | 16100 |
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.
