U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Metagenome-assembled genome: ERR5385024_bin.7_metawrap_v1.3.0_MAG

Identifiers
BioSample: SAMEA110698788; SRA: ERS12796326
Organism
uncultured Variovorax sp.
cellular organisms; Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Variovorax; environmental samples
Attributes
broad-scale environmental contextplant
collection date2017-10-17
environmental mediumrhizosphere
geographic locationUnited Kingdom
investigation typemetagenome-assembled genome
isolation sourcerhizosphere metagenome
project nameThe microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development and health. These microbial communities are not stochastically assembled from the surrounding soil but their composition and function is controlled, at least partially, by the host plant. Here we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. This library contains shotgun metagenomics sequencing from bulk (quarryfield) soil, a modern elite line (Morex) and two wild genotypes: B1K-12 (referered to as Desert), and B1K-31 (referred to as 'North')
sample nameERR5385024_bin.7_metawrap_v1.3.0_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2022-08-24
ENA-LAST-UPDATE2022-08-24
External IdSAMEA110698788
INSDC center aliasEMG
INSDC center nameEMG
INSDC first public2022-08-24T12:18:13Z
INSDC last update2022-08-24T12:18:13Z
INSDC statuspublic
Submitter IdERR5385024_bin.7_metawrap_v1.3.0_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaSPAdes v3.15.3
binning parametersMaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning softwaremetawrap v1.3.0
broker nameEMG broker account, EMBL-EBI
completeness score87.2
completeness softwareCheckM
contamination score0.88
geographic location (latitude)56.45139
geographic location (longitude)3.074722
local environmental contextbarley
metagenomic sourcerhizosphere metagenome
sample derived fromSAMEA8103263
sequencing methodNextSeq 500
taxonomic classificationThe taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Variovorax;s__
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR5385024 of study ERP113334.

BioProject
PRJEB55045
Retrieve all samples from this project

Submission
EBI; 2022-08-25
Accession:
SAMEA110698788
ID:
30495837

BioProject Nucleotide

Supplemental Content

Related information

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
You are here: NCBI > DNA & RNA > BioSample
Support Center