Genome assembly ASM393602v1
- NCBI RefSeq assembly
- GCF_003936025.1
- Submitted GenBank assembly
- GCA_003936025.1
- Taxon
- Stutzerimonas stutzeri
- Strain
- PS_138
- WGS project
- RHRE01
- Submitter
- Washington University in St. Louis School of Medicine
- Date
- Dec 11, 2018
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 4.4 Mb | 4.4 Mb |
Total ungapped length | 4.4 Mb | 4.4 Mb |
Number of scaffolds | 52 | 52 |
Scaffold N50 | 168.6 kb | 168.6 kb |
Scaffold L50 | 8 | 8 |
Number of contigs | 56 | 56 |
Contig N50 | 157.5 kb | 157.5 kb |
Contig L50 | 9 | 9 |
GC percent | 64 | 64 |
Genome coverage | 28.0x | 28.0x |
Assembly level | Scaffold | Scaffold |
Sample details
- BioSample ID
- SAMN10249100
- Description
- Microbe sample from Stutzerimonas stutzeri
- Submitter
- Washington University in St. Louis School of Medicine
- Strain
- PS_138
- Isolation source
- nursing call button in hospital intensive care unit
- Collection date
- 2016-04
- Geographic location
- Pakistan
- Sample type
- whole organism
- Relative week
- 12
- Collection room
- PAK-2
- Sample name
- PS_138
- SRA
- SRS5369388
- Models
- Microbe, viral or environmental
- Package
- Microbe.1.0
- Submission date
- 2018-10-16T18:54:07.316
- Publication date
- 2018-12-08T00:00:00.000
- Last updated
- 2022-07-29T21:06:01.098
Assembly methods
- Sequencing technology
- Illumina NextSeq
- Comment
- Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
- Assembly method
- SPAdes v. 3.11.0
Additional genomes
Browse all Stutzerimonas stutzeri genomes (726)BioProject
PRJNA497126Pakistan and United States ICU transmission dynamics
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_003936025.1-RS_2024_03_12 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Mar 12, 2024 | Nov 9, 2018 |
Genes | 4,100 | 4,099 |
Protein-coding | 3,985 | 3,962 |
Software version | 6.7 | 4.6 |
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 (v1.2.3)
Completeness: 99.4% (39th Percentile)
Contamination: 0.02%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Pseudomonas stutzeri 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
- Stutzerimonas stutzeri
- Submitted species name
- Stutzerimonas stutzeri
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_000219605.1 | GCA_000219605.1 |
Organism name | Stutzerimonas stutzeri | Stutzerimonas stutzeri |
Type category | type | type |
ANI | 97.56% | 97.56% |
Assembly coverage | 89.73% | 89.73% |
Type assembly coverage | 85.98% | 85.98% |
Chromosomes
Note: This scaffold-level genome assembly includes 52 scaffolds and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_003936025.1 | GCF_003936025.1 | ASM393602v1 | Scaffold | Dec 11, 2018 |