U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Rumen Uncultured Genome RUG14080

Identifiers
BioSample: SAMEA6152218; SRA: ERS3952253
Organism
Campylobacter fetus
cellular organisms; Bacteria; Pseudomonadati; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae; Campylobacter
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 nameRUG14080
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2019-11-14T04:04:37Z
ENA-LAST-UPDATE2019-11-01T20:36:18Z
External IdSAMEA6152218
INSDC center nameTHE ROSLIN INSTITUTE
INSDC first public2019-11-14T04:04:37Z
INSDC last update2019-11-01T20:36:18Z
INSDC statuspublic
Submitter IdRUG14080
assembly qualityMultiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs
assembly softwareMEGAHIT; v1.1.1; --kmin-1pass, -m 60e+10, --k-list 27,37,47,57,67,77,87, --min-contig-len 1000, -t 16
binning parameterstetra-nucleotide frequencies and abundance
binning softwareMetaBAT2
completeness score97.76
completeness softwareCheckM
contamination score0.37
geographic location (latitude)55.861398
geographic location (longitude)-3.206493
metagenomic sourcebovine gut metagenome
sample derived fromERS3622879
scientific_nameCampylobacter fetus
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 RUG14080 Campylobacter fetus

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

Submission
EBI; 2019-11-17
Accession:
SAMEA6152218
ID:
13309307

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Support Center