Genome assembly ASM1927275v1

Actions
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

RefSeqGenBank
Genome size5.4 Mb5.4 Mb
Total ungapped length4.8 Mb4.8 Mb
Number of chromosomes22
Number of scaffolds22
Scaffold N503.6 Mb3.6 Mb
Scaffold L5011
Number of contigs371371
Contig N50102.5 kb102.5 kb
Contig L501616
GC percent45.545.5
Genome coverage86.4x86.4x
Assembly levelChromosomeChromosome

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

PRJNA668870

Whole genome Sequencing for food-borne outbreaks in Thailand

Pathogen Detection Resource

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_019272755.1-RS_2024_08_19
DateAug 19, 2024
Genes4,453
Protein-coding4,219
Software version6.8

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.

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Quality 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 organismBest match type-strain
Type assemblyGCA_001558495.2GCA_001558495.2
Organism nameVibrio parahaemolyticusVibrio parahaemolyticus
Type categorytypetype
ANI98.57%98.57%
Assembly coverage98.25%98.25%
Type assembly coverage91.78%91.78%

Chromosomes

Chromosome
GenBank
RefSeq
Size (bp)
GC content (%)
Unlocalized count
Action
1CP078693.1NZ_CP078693.13,577,84845.50
2CP078694.1NZ_CP078694.11,814,24645.50

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_019272755.1GCF_019272755.1ASM1927275v1ChromosomeJul 19, 2021