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Rumen Uncultured Genome RUG12595

Identifiers
BioSample: SAMEA6150731; SRA: ERS3950768
Organism
uncultured Lachnospiraceae bacterium
cellular organisms; Bacteria; Bacillati; 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 nameRUG12595
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2019-11-14T04:04:37Z
ENA-LAST-UPDATE2019-11-01T20:34:58Z
External IdSAMEA6150731
INSDC center nameTHE ROSLIN INSTITUTE
INSDC first public2019-11-14T04:04:37Z
INSDC last update2019-11-01T20:34:58Z
INSDC statuspublic
Submitter IdRUG12595
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 score84.89
completeness softwareCheckM
contamination score3.32
geographic location (latitude)55.861398
geographic location (longitude)-3.206493
metagenomic sourcebovine gut metagenome
sample derived fromERS3622328
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 RUG12595 uncultured Lachnospiraceae bacterium

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

Submission
EBI; 2019-11-17
Accession:
SAMEA6150731
ID:
13314219

BioProject Nucleotide

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