We’re soliciting feedback from JGI primary and data users on JGI Data Release and Utilization policies. Fill out our Request for Information by April 21.
Info • Symbiochloris reticulata Switzerland 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 photobiont genome. The aligned Illumina gDNAs were assembled with Velvet and then AllPathsLG. The mitochondrial and chloroplast assemblies are available on the Download page.

Annotation v1 is a draft annotation using an extracted metatranscriptome and the JGI Annotation Pipeline v1.10. The metatranscriptome was extracted by aligning the reads with the extracted photobiont genome. The aligned Illumina reads were assemblied with Trinity.

Summary statistics for the Symbiochloris reticulata Switzerland v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 59.35
Sequencing read coverage depth 109.9x
# of contigs 2324
# of scaffolds 1891
# of scaffolds >= 2Kbp 1891
Scaffold N50 314
Scaffold L50 (Mbp) 0.06
# of gaps 433
% of scaffold length in gaps 0.8%
Three largest Scaffolds (Mbp) 0.28, 0.24, 0.24


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 22012449 21105161 95.9%
Other JGI_RNA_contigs 72939 62350 85.5%


Gene Models FilteredModels1
length (bp) of: average median
gene 2829 2220
transcript 1367 1180
exon 203 161
intron 256 243
description:
protein length (aa) 376 303
exons per gene 6.75 6
# of gene models 12701


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.