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Rumen Uncultured Genome RUG11942

Identifiers
BioSample: SAMEA6150077; SRA: ERS3950115
Organism
uncultured Bacteroidota bacterium
cellular organisms; Bacteria; Pseudomonadati; FCB group; Bacteroidota/Chlorobiota group; Bacteroidota; 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 nameRUG11942
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2019-11-13T17:04:45Z
ENA-LAST-UPDATE2019-11-01T20:34:27Z
External IdSAMEA6150077
INSDC center nameTHE ROSLIN INSTITUTE
INSDC first public2019-11-13T17:04:45Z
INSDC last update2019-11-01T20:34:27Z
INSDC statuspublic
Submitter IdRUG11942
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 score86.2
completeness softwareCheckM
contamination score3.23
geographic location (latitude)55.861398
geographic location (longitude)-3.206493
metagenomic sourcebovine gut metagenome
sample derived fromERS3619959
scientific_nameuncultured Bacteroidetes 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 RUG11942 uncultured Bacteroidetes bacterium

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

Submission
EBI; 2019-11-17
Accession:
SAMEA6150077
ID:
13313566

BioProject Nucleotide

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