Rumen Uncultured Genome RUG10728

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Result Filters

Identifiers: BioSample: SAMEA6148861; SRA: ERS3948901

Organism: Ruminococcus flavefaciens
cellular organisms; Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales; Oscillospiraceae; Ruminococcus

Attributes

collection date	not collected
broad-scale environmental context	Bos taurus
local-scale environmental context	stomach
environmental medium	bodily fluid
geographic location	United Kingdom
investigation type	metagenome
isolation source	cattle rumen
project name	Metagenomic sequencing of the rumen of 240 cattle from Scotland
reference for biomaterial	Stewart 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 name	RUG10728
ENA-CHECKLIST	ERC000047
ENA-FIRST-PUBLIC	2019-11-13T17:04:45Z
ENA-LAST-UPDATE	2019-11-01T20:33:49Z
External Id	SAMEA6148861
INSDC center name	THE ROSLIN INSTITUTE
INSDC first public	2019-11-13T17:04:45Z
INSDC last update	2019-11-01T20:33:49Z
INSDC status	public
Submitter Id	RUG10728
assembly quality	Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs
assembly software	IDBA-UD; v1.1.3; --num_threads 16 --pre_correction --min_contig 300
binning parameters	tetra-nucleotide frequencies and abundance
binning software	MetaBAT2
completeness score	97.22
completeness software	CheckM
contamination score	1.57
geographic location (latitude)	55.861398
geographic location (longitude)	-3.206493
metagenomic source	bovine gut metagenome
sample derived from	ERS3610015
scientific_name	Ruminococcus flavefaciens
sequencing method	Illumina HiSeq 4000
taxonomic identity marker	multi-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