Genome assembly ASM1927275v1
- NCBI RefSeq assembly
- GCF_019272755.1
- Submitted GenBank assembly
- GCA_019272755.1
- Taxon
- Vibrio parahaemolyticus
- Strain
- Colony12
- Submitter
- Ministry of Public Health-Thailand
- Date
- Jul 19, 2021
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 5.4 Mb | 5.4 Mb |
Total ungapped length | 4.8 Mb | 4.8 Mb |
Number of chromosomes | 2 | 2 |
Number of scaffolds | 2 | 2 |
Scaffold N50 | 3.6 Mb | 3.6 Mb |
Scaffold L50 | 1 | 1 |
Number of contigs | 371 | 371 |
Contig N50 | 102.5 kb | 102.5 kb |
Contig L50 | 16 | 16 |
GC percent | 45.5 | 45.5 |
Genome coverage | 86.4x | 86.4x |
Assembly level | Chromosome | Chromosome |
Sample details
- BioSample ID
- SAMN17831976
- Description
- Pathogen: environmental/food/other sample from Vibrio parahaemolyticus
- Submitter
- Ministry of Public Health-Thailand
- Strain
- Colony12
- Collected by
- Department of Disease Control, Ministry of Public Health
- Collection date
- Aug 17, 2019
- Geographic location
- Thailand: Nhong Khai
- Latitude and longitude
- Not applicable
- Isolation source
- Rectal Swab
- Sample name
- Colony12
- Models
- Pathogen.env
- Package
- Pathogen.env.1.0
- Submission date
- 2021-02-07T23:54:04.780
- Publication date
- 2021-02-07T00:00:00.000
- Last updated
- 2021-07-12T07:09:21.846
Assembly methods
- Sequencing technology
- Illumina HiSeq
- Assembly method
- idba_ud v. V1.1.3
BioProject
PRJNA668870Whole genome Sequencing for food-borne outbreaks in Thailand
Pathogen Detection Resource
Annotation details
RefSeq | |
---|---|
Provider | NCBI RefSeq |
Name | GCF_019272755.1-RS_2024_08_19 |
Date | Aug 19, 2024 |
Genes | 4,453 |
Protein-coding | 4,219 |
Software version | 6.8 |
About PGAP
The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) uses multiple approaches to predict protein-coding and RNA genes and other functional elements directly from sequence.
Continue readingQuality analysis
CheckM analysis (v1.2.3)
Completeness: 97.57% (11st Percentile)
Contamination: 1.77%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Vibrio parahaemolyticus CheckM marker set. For more information on CheckM, see Parks, et al. Genome Res (2015).
Taxonomy check
- Taxonomy check status
- OK
- Best match status
- species_match
- Submitted organism name
- Vibrio parahaemolyticus
- Submitted species name
- Vibrio parahaemolyticus
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_001558495.2 | GCA_001558495.2 |
Organism name | Vibrio parahaemolyticus | Vibrio parahaemolyticus |
Type category | type | type |
ANI | 98.57% | 98.57% |
Assembly coverage | 98.25% | 98.25% |
Type assembly coverage | 91.78% | 91.78% |
Chromosomes
Chromosome | GenBank | RefSeq | Size (bp) | GC content (%) | Unlocalized count | Action |
---|---|---|---|---|---|---|
1 | CP078693.1 | NZ_CP078693.1 | 3,577,848 | 45.5 | 0 | |
2 | CP078694.1 | NZ_CP078694.1 | 1,814,246 | 45.5 | 0 |
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_019272755.1 | GCF_019272755.1 | ASM1927275v1 | Chromosome | Jul 19, 2021 |