Genome assembly ASM4008171v1

Actions
NCBI RefSeq assembly
GCF_000733315.1
Submitted GenBank assembly
GCA_000733315.1
Taxon
Vibrio sp. ER1A
Strain
ER1A
WGS project
JPJA01
Submitter
Institute of Marine and Environmental Technology
Date
Jul 25, 2014

Assembly statistics

RefSeq
Genome size6.6 Mb
Total ungapped length6.1 Mb
Number of scaffolds108
Scaffold N50394.3 kb
Scaffold L504
Number of contigs211
Contig N5068.3 kb
Contig L5026
GC percent44
Genome coverage140.0x
Assembly levelScaffold

Sample details

BioSample ID
SAMN02898119
Description
Microbe sample from Vibrio sp. ER1A
Submitter
Institute of Marine and Environmental Technology
Strain
ER1A
Collection date
2005
Geographic location
USA: Hawaii, Honolulu, Black Point Bay
Host
Elysia rufescens
Sample name
Vibrio sp. strain ER1A
Models
Microbe, viral or environmental
Package
Microbe.1.0
Submission date
2014-06-30T14:10:13.550
Publication date
2014-07-01T12:44:06.370
Last updated
2014-11-06T17:12:18.160

Assembly methods

Sequencing technology
Illumina MiSeq
Comment
Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
Assembly method
CLC Genomics v. April 2014

Additional genomes

Browse all Vicinamibacterales bacterium genomes (1)

BioProject

PRJNA253939

Vibrio sp. ER1A Genome sequencing and assembly

Annotation details

RefSeq
ProviderNCBI RefSeq
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateJan 25, 2024
Genes5,712
Protein-coding5,523
Software version6.6

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 reading

Quality analysis

CheckM analysis (v1.2.2)

Completeness: 99.43% (100th Percentile)

Contamination: 1.63%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Vibrio 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
Vibrio sp. ER1A
Submitted species name
Vibrio sp. ER1A

Average Nucleotide Identity (ANI) match details

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

n/a

GCA_900088415.1
Organism name

n/a

Vibrio mediterranei
Type category

n/a

type
ANI

n/a

98.13%
Assembly coverage

n/a

81.64%
Type assembly coverage

n/a

87.74%

Chromosomes

Note: This scaffold-level genome assembly includes 108 scaffolds and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_040081715.1

n/a

ASM4008171v1ContigJun 5, 2024