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Rumen Uncultured Genome RUG13896

Identifiers
BioSample: SAMEA6152034; SRA: ERS3952069
Organism
uncultured Lachnospiraceae bacterium
cellular organisms; Bacteria; Terrabacteria group; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae; 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 nameRUG13896
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2019-11-14T04:04:37Z
ENA-LAST-UPDATE2019-11-01T20:35:52Z
External IdSAMEA6152034
INSDC center nameTHE ROSLIN INSTITUTE
INSDC first public2019-11-14T04:04:37Z
INSDC last update2019-11-01T20:35:52Z
INSDC statuspublic
Submitter IdRUG13896
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 score83.84
completeness softwareCheckM
contamination score5.31
geographic location (latitude)55.861398
geographic location (longitude)-3.206493
metagenomic sourcebovine gut metagenome
sample derived fromERS3615451
scientific_nameuncultured Lachnospiraceae 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 RUG13896 uncultured Lachnospiraceae bacterium

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

Submission
EBI; 2019-11-17
Accession:
SAMEA6152034
ID:
13309123

BioProject Nucleotide

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