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Rumen Uncultured Genome RUG11653

Identifiers
BioSample: SAMEA6149788; SRA: ERS3949826
Organism
uncultured Bacteroidia bacterium
cellular organisms; Bacteria; FCB group; Bacteroidota/Chlorobiota group; Bacteroidota; Bacteroidia; 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 nameRUG11653
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2019-11-13T17:04:44Z
ENA-LAST-UPDATE2019-11-01T20:34:22Z
External IdSAMEA6149788
INSDC center nameTHE ROSLIN INSTITUTE
INSDC first public2019-11-13T17:04:44Z
INSDC last update2019-11-01T20:34:22Z
INSDC statuspublic
Submitter IdRUG11653
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 score86.28
completeness softwareCheckM
contamination score4.84
geographic location (latitude)55.861398
geographic location (longitude)-3.206493
metagenomic sourcebovine gut metagenome
sample derived fromERS3626449
scientific_nameuncultured Bacteroidia bacterium
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 RUG11653 uncultured Bacteroidia bacterium

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

Submission
EBI; 2019-11-17
Accession:
SAMEA6149788
ID:
13313277

BioProject Nucleotide

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