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Info • Lobaria pulmonaria Scotland extracted metagenome v1.0

Status

[March 2018] Assembly v1 is a minimal 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 on the Download page.

Annotation v1 is a draft annotation, using an extracted metatranscriptome, the reference mycobiont transcriptome, and the JGI Annotation Pipeline v1.10. The metatranscriptome was extracted by aligning the Illumina reads with the extracted mycobiont genome. The metatranscriptome and the reference transcriptome were each assemblied separately with Trinity.

Summary statistics for the Lobaria pulmonaria Scotland v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 55.85
Sequencing read coverage depth 144.8x
# of contigs 1603
# of scaffolds 1189
# of scaffolds >= 2Kbp 1189
Scaffold N50 184
Scaffold L50 (Mbp) 0.08
# of gaps 414
% of scaffold length in gaps 0.4%
Three largest Scaffolds (Mbp) 0.49, 0.47, 0.46


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 371979111 365166762 98.2%
Other JGI_met_RNA_contigs 88215 80443 91.2%
Other JGI_ref_RNA_contigs 103899 78854 75.9%


Gene Models FilteredModels1
length (bp) of: average median
gene 1553 1327
transcript 1384 1150
exon 469 291
intron 88 60
description:
protein length (aa) 392 306
exons per gene 2.95 2
# of gene models 16471


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.