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Info • Lobaria pulmonaria Africa 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 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.