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Rumen Uncultured Genome RUG10281

Identifiers
BioSample: SAMEA6148414; SRA: ERS3948454
Organism
Ruminococcus flavefaciens
cellular organisms; Bacteria; Terrabacteria group; Bacillota; Clostridia; Eubacteriales; Oscillospiraceae; Ruminococcus
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 nameRUG10281
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2019-11-13T17:04:45Z
ENA-LAST-UPDATE2019-11-01T20:33:41Z
External IdSAMEA6148414
INSDC center nameTHE ROSLIN INSTITUTE
INSDC first public2019-11-13T17:04:45Z
INSDC last update2019-11-01T20:33:41Z
INSDC statuspublic
Submitter IdRUG10281
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 score82.1
completeness softwareCheckM
contamination score1.4
geographic location (latitude)55.861398
geographic location (longitude)-3.206493
metagenomic sourcebovine gut metagenome
sample derived fromERS3618043
scientific_nameRuminococcus flavefaciens
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 RUG10281 Ruminococcus flavefaciens

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

Submission
EBI; 2019-11-17
Accession:
SAMEA6148414
ID:
13311908

BioProject Nucleotide

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