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Metagenome-Assembled Genome: DRR247343_bin.58_MetaWRAP_v1.3_MAG

Identifiers
BioSample: SAMEA114447662; SRA: ERS16434306
Organism
Sphingobium yanoikuyae
cellular organisms; Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingobium
Attributes
broad-scale environmental contexthuman digestive system
collection datenot provided
environmental mediumsaliva
geographic locationnot provided
investigation typemetagenome-assembled genome
isolation sourceoral metagenome
project nameDeep shotgun metagenome sequencing (>10 Gb per sample) of bulk DNA extracted from saliva of MRONJ patients and healthy controls (initially 5 vs 5 individuals) was performed to overcome limitations of prior studies explored the association between MRONJ and microbial or viral infection. The sequence data after the preprocessing and removal of human reads are registered, including those of additional 5 patients.
sample nameDRR247343_bin.58_MetaWRAP_v1.3_MAG
ENA-CHECKLISTERC000047
INSDC center nameEMG
Submitter IdDRR247343_bin.58_MetaWRAP_v1.3_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
broker nameEBI-EMG
completeness score50.36
completeness softwareCheckM
contamination score1.25
geographic location (latitude)not provided
geographic location (longitude)not provided
local environmental contextoral cavity
metagenomic sourceoral metagenome
sample derived fromSAMD00248606
scientific_nameSphingobium yanoikuyae
sequencing methodHiSeq X Ten
taxonomic classificationThe taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium;s__Sphingobium yanoikuyae
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run DRR247343 of study DRP006591.

BioProject
PRJEB56901
Retrieve all samples from this project

Submission
EBI; 2023-09-29
Accession:
SAMEA114447662
ID:
37603823

BioProject Nucleotide

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