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Info • Lobaria pulmonaria Spain extracted metagenome v1.0

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 on the Download page.

Annotation v1 is a draft annotation, using the reference mycobiont transcriptome and the JGI Annotation Pipeline v1.10.

Summary statistics for the Lobaria pulmonaria Spain v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 55.60
Sequencing read coverage depth 145.9x
# of contigs 1672
# of scaffolds 1257
# of scaffolds >= 2Kbp 1257
Scaffold N50 197
Scaffold L50 (Mbp) 0.08
# of gaps 415
% of scaffold length in gaps 0.4%
Three largest Scaffolds (Mbp) 0.55, 0.47, 0.44


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 169390194 163301748 96.4%
Other JGI_RNA_contigs 103899 77914 75.0%


Gene Models FilteredModels1
length (bp) of: average median
gene 1535 1296
transcript 1371 1132
exon 465 288
intron 86 60
description:
protein length (aa) 393 307
exons per gene 2.95 2
# of gene models 16296


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.