Genome assembly ASM296474v1

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NCBI RefSeq assembly
GCF_002964745.1
Submitted GenBank assembly
GCA_002964745.1
Taxon
Pseudoalteromonas sp. T1lg24
Strain
T1lg24
WGS project
PQCB01
Submitter
Zhejiang University of Technology
Date
Feb 28, 2018

Assembly statistics

RefSeqGenBank
Genome size4.7 Mb4.7 Mb
Total ungapped length4.7 Mb4.7 Mb
Number of scaffolds3535
Scaffold N50856.6 kb856.6 kb
Scaffold L5022
Number of contigs5858
Contig N50260.3 kb260.3 kb
Contig L5066
GC percent4141
Genome coverage12.0x12.0x
Assembly levelScaffoldScaffold
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN08380956
Description
Microbe sample from pseudoalteromonas
Comment
pseudoalteromonas
Submitter
Zhejiang University of Technology
Strain
T1lg24
Isolation source
seawater at sediment depth
Collection date
Mar 20, 2016
Geographic location
China: Zhejiang Province, Ximen Island
Sample type
whole organism
Biomaterial provider
lab
Collected by
Yangcao
Culture collection
not collected
Broad-scale environmental context
Mangrove forest
Genotype
DNA
Identified by
Yajuanding
Lab host
none
Latitude and longitude
28.33 N 121.18 E
Sample size
4.7Mb
Temperature
28
Sample name
T1lg24
Models
Microbe, viral or environmental
Package
Microbe.1.0
Submission date
2018-01-19T21:15:05.340
Publication date
2018-01-19T00:00:00.000
Last updated
2021-02-28T05:24:18.217

Assembly methods

Sequencing technology
Illumina HiSeq
Assembly method
Velvet v. 2.3

BioProject

PRJNA430938

Pseudoalteromonas sp. T1lg24 Genome sequencing and assembly

Publications

Showing 1 of 1

View in PubMed

Annotation details

RefSeq
ProviderNCBI RefSeq
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateJan 17, 2024
Genes4,305
Protein-coding4,119
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: 97.67% (100th Percentile)

Contamination: 0.63%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Pseudoalteromonas 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
Pseudoalteromonas sp. T1lg24
Submitted species name
Pseudoalteromonas sp. T1lg24

Average Nucleotide Identity (ANI) match details

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

n/a

GCA_000238255.4
Organism name

n/a

Pseudoalteromonas spongiae
Type category

n/a

type
ANI

n/a

96.47%
Assembly coverage

n/a

88.83%
Type assembly coverage

n/a

87.68%

Chromosomes

Note: This scaffold-level genome assembly includes 35 scaffolds and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002964745.1GCF_002964745.1ASM296474v1ScaffoldFeb 28, 2018