Genome assembly ASM296474v1
- 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
RefSeq | GenBank | |
---|---|---|
Genome size | 4.7 Mb | 4.7 Mb |
Total ungapped length | 4.7 Mb | 4.7 Mb |
Number of scaffolds | 35 | 35 |
Scaffold N50 | 856.6 kb | 856.6 kb |
Scaffold L50 | 2 | 2 |
Number of contigs | 58 | 58 |
Contig N50 | 260.3 kb | 260.3 kb |
Contig L50 | 6 | 6 |
GC percent | 41 | 41 |
Genome coverage | 12.0x | 12.0x |
Assembly level | Scaffold | Scaffold |
View sequences | view RefSeq sequences | view 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
Additional genomes
Browse all Pseudoalteromonas sp. T1lg24 genomes (1)Publications
RefSeq microbial genomes database: new representation and annotation strategy
T Tatusova, et al.
Annotation details
RefSeq | |
---|---|
Provider | NCBI RefSeq |
Name | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Jan 17, 2024 |
Genes | 4,305 |
Protein-coding | 4,119 |
Software version | 6.6 |
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 readingQuality 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 organism | Best 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_002964745.1 | GCF_002964745.1 | ASM296474v1 | Scaffold | Feb 28, 2018 |