Info • Symbiochloris reticulata Spain extracted metagenome v1.0


[March 2018] Assembly v1 is a 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 the reference photobiont metatranscriptome and the JGI Annotation Pipeline v1.10.

Summary statistics for the Symbiochloris reticulata Spain v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 56.84
Sequencing read coverage depth ??x
# of contigs 3175
# of scaffolds 3105
# of scaffolds >= 2Kbp 3105
Scaffold N50 576
Scaffold L50 (Mbp) 0.03
# of gaps 70
% of scaffold length in gaps 0.1%
Three largest Scaffolds (Mbp) 0.17, 0.15, 0.15

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 139268010 116611620 83.7%
Other JGI_RNA_contigs 102102 56657 55.5%

Gene Models FilteredModels1
length (bp) of: average median
gene 2825 2257
transcript 1344 1161
exon 200 158
intron 261 246
protein length (aa) 373 307
exons per gene 6.71 6
# of gene models 12144


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.