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Rumen Uncultured Genome RUG12218

Identifiers
BioSample: SAMEA6150353; SRA: ERS3950391
Organism
uncultured Ruminococcus sp.
cellular organisms; Bacteria; Terrabacteria group; Bacillota; Clostridia; Eubacteriales; Oscillospiraceae; Ruminococcus; environmental samples
Attributes
collection datenot collected
broad-scale environmental contextBos taurus
local-scale environmental contextstomach
environmental mediumbodily fluid
geographic locationUnited Kingdom
investigation typemetagenome
isolation sourcecattle rumen
project nameMetagenomic sequencing of the rumen of 240 cattle from Scotland
reference for biomaterialStewart RD, Auffret MD, Warr A, Walker AW, Roehe R, Watson M. Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. (2019) Nat Biotechnol. 37(8):953-961. doi: 10.1038/s41587-019-0202-3.
sample nameRUG12218
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2019-11-14T04:04:37Z
ENA-LAST-UPDATE2019-11-01T20:34:49Z
External IdSAMEA6150353
INSDC center nameTHE ROSLIN INSTITUTE
INSDC first public2019-11-14T04:04:37Z
INSDC last update2019-11-01T20:34:49Z
INSDC statuspublic
Submitter IdRUG12218
assembly qualityMultiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs
assembly softwareIDBA-UD; v1.1.3; --num_threads 16 --pre_correction --min_contig 300
binning parameterstetra-nucleotide frequencies and abundance
binning softwareMetaBAT2
completeness score82.81
completeness softwareCheckM
contamination score3.81
geographic location (latitude)55.861398
geographic location (longitude)-3.206493
metagenomic sourcebovine gut metagenome
sample derived fromERS3621012
scientific_nameuncultured Ruminococcus sp.
sequencing methodIllumina HiSeq 4000
taxonomic identity markermulti-marker approach - MAGpy - Stewart RD, Auffret MD, Snelling TJ, Roehe R, Watson M. (2019) MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). Bioinformatics. 35(12):2150-2152. doi: 10.1093/bioinformatics/bty905
Description

Cattle rumen microbiome RUG RUG12218 uncultured Ruminococcus sp.

BioProject
PRJEB31266 Metagenomic sequencing of cattle
Retrieve all samples from this project

Submission
EBI; 2019-11-17
Accession:
SAMEA6150353
ID:
13313842

BioProject Nucleotide

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