Genome assembly SRR5395413_bin.24_MetaWRAP_v1.3_MAG
- 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 size | 1.5 Mb |
Total ungapped length | 1.5 Mb |
Number of contigs | 99 |
Contig N50 | 37.6 kb |
Contig L50 | 13 |
GC percent | 39 |
Genome coverage | 31.0x |
Assembly level | Contig |
View sequences | view 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
Additional genomes
Browse all uncultured Veillonella sp. genomes (274)BioProject
PRJEB56889EMG 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 organism | Best 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_MAG | Contig | Oct 1, 2023 |