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Rumen Uncultured Genome RUG10427

Identifiers
BioSample: SAMEA6148560; SRA: ERS3948600
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 nameRUG10427
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2019-11-13T17:04:45Z
ENA-LAST-UPDATE2019-11-01T20:33:43Z
External IdSAMEA6148560
INSDC center nameTHE ROSLIN INSTITUTE
INSDC first public2019-11-13T17:04:45Z
INSDC last update2019-11-01T20:33:43Z
INSDC statuspublic
Submitter IdRUG10427
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 score81.8
completeness softwareCheckM
contamination score2.03
geographic location (latitude)55.861398
geographic location (longitude)-3.206493
metagenomic sourcebovine gut metagenome
sample derived fromERS3618531
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 RUG10427 uncultured Ruminococcus sp.

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

Submission
EBI; 2019-11-17
Accession:
SAMEA6148560
ID:
13312054

BioProject Nucleotide

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