Genome assembly SRR5395413_bin.24_MetaWRAP_v1.3_MAG

FTP
Actions
Submitted GenBank assembly
GCA_963534055.1
Taxon
uncultured Veillonella sp.
Isolate
SRR5395413_bin.24_MetaWRAP_v1.3_MAG
WGS project
CAUSQR01
Submitter
EMG
Date
Oct 1, 2023

Genome notes

NCBI has noted the following for this genome assembly. View definitions

  • annotation fails MAG completeness check
  • derived from metagenome

Assembly statistics

GenBank
Genome size1.5 Mb
Total ungapped length1.5 Mb
Number of contigs99
Contig N5037.6 kb
Contig L5013
GC percent39
Genome coverage31.0x
Assembly levelContig
View sequencesview GenBank sequences

Sample details

BioSample ID
SAMEA114447102
Description
Metagenome-Assembled Genome: SRR5395413_bin.24_MetaWRAP_v1.3_MAG
Comment
This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR5395413 of study SRP102724.
Submitter
EBI
ENA-CHECKLIST
ERC000047
INSDC center name
EMG
Submitter Id
SRR5395413_bin.24_MetaWRAP_v1.3_MAG
Assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
Assembly software
metaSPAdes v3.15.3
Binning parameters
MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
Binning software
MetaWRAP v1.3
Broad-scale environmental context
human digestive system
Broker name
EBI-EMG
Completeness score
86.53
Completeness software
CheckM
Contamination score
0.3
Environmental medium
saliva
Investigation type
metagenome-assembled genome
Isolation source
oral metagenome
Local environmental context
oral cavity
Metagenomic source
oral metagenome
Project name
salivary metagenomic in Chinese Children
Sample derived from
SAMN06646483
Sample name
SRR5395413_bin.24_MetaWRAP_v1.3_MAG
Scientific name
uncultured Veillonella sp.
Sequencing method
Illumina HiSeq 2500
Taxonomic classification
The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella;s__
Taxonomic identity marker
multi-marker approach
SRA
ERS16433746
Models
Generic
Package
Generic.1.0
Submission date
2023-09-29T08:16:48.310
Publication date
2023-09-28T00:00:00.000
Last updated
2023-09-28T10:29:18.000

Assembly methods

Sequencing technology
Illumina HiSeq 2500
Comment
This is an EMG-produced Third Party Annotation (TPA) bin derived from the primary whole genome shotgun (WGS) data set SRP102724. This sample represents a Metagenome-Assembled Genome (MAG) from the metagenomic run SRR5395413.
Assembly method
metaSPAdes v3.15.3

BioProject

PRJEB56889

EMG produced TPA metagenomics assembly of PRJNA380727 data set (human saliva metagenome Raw sequence reads).

Quality analysis

CheckM analysis (v1.2.2)

Completeness: 80% (39th Percentile)

Contamination: 0.62%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Veillonella CheckM marker set. For more information on CheckM, see Parks, et al. Genome Res (2015).

Taxonomy check

Taxonomy check status
OK
Best match status
genus_match
Submitted organism name
uncultured Veillonella sp.
Submitted species name
uncultured Veillonella sp.

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assembly

n/a

GCA_002959775.1
Organism name

n/a

Veillonella rogosae
Type category

n/a

type
ANI

n/a

93.99%
Assembly coverage

n/a

92.77%
Type assembly coverage

n/a

65.7%

Chromosomes

Note: This contig-level genome assembly includes 99 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_963534055.1

n/a

SRR5395413_bin.24_MetaWRAP_v1.3_MAGContigOct 1, 2023