Genome assembly ASM4109117v1
- NCBI RefSeq assembly
- GCF_041091175.1
- Submitted GenBank assembly
- GCA_041091175.1
- Taxon
- Providencia manganoxydans
- Strain
- fly-242
- WGS project
- JBFZNR01
- Submitter
- The Hong Kong Polytechnic University
- Date
- Aug 7, 2024
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 4.8 Mb | 4.8 Mb |
Total ungapped length | 4.8 Mb | 4.8 Mb |
Number of scaffolds | 104 | 104 |
Scaffold N50 | 177.1 kb | 177.1 kb |
Scaffold L50 | 9 | 9 |
Number of contigs | 115 | 115 |
Contig N50 | 149 kb | 149 kb |
Contig L50 | 11 | 11 |
GC percent | 40.5 | 40.5 |
Genome coverage | 200.0x | 200.0x |
Assembly level | Scaffold | Scaffold |
View sequences | view RefSeq sequences |
Sample details
- BioSample ID
- SAMN40659674
- Description
- Pathogen: environmental/food/other sample from Providencia manganoxydans
- Submitter
- The Hong Kong Polytechnic University
- Strain
- fly-242
- Collected by
- Rong Zhang
- Collection date
- 2023
- Geographic location
- China:Shandong
- Isolation source
- fly
- Latitude and longitude
- 36.68 N 117.00 E
- Sample name
- fly-242
- Models
- Pathogen.env
- Package
- Pathogen.env.1.0
- Submission date
- 2024-03-30T03:46:07.247
- Publication date
- 2024-03-30T00:00:00.000
- Last updated
- 2024-03-30T04:01:22.227
Assembly methods
- Sequencing technology
- Illumina HiSeq
- Comment
- The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
- Assembly method
- SPAdes v. v3.13.1
Additional genomes
Browse all Providencia manganoxydans genomes (55)BioProject
PRJNA1093566Role of Flies in the Dissemination of Carbapenem-Resistant Enterobacteriaceae (CRE): An Epidemiological and Genomic Study in China
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_041091175.1-RS_2024_08_08 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Aug 8, 2024 | Aug 2, 2024 |
Genes | 4,489 | 4,488 |
Protein-coding | 4,311 | 4,327 |
Software version | 6.7 | 6.7 |
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: 98.34% (18th Percentile)
Contamination: 3.5%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Providencia 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
- Providencia manganoxydans
- Submitted species name
- Providencia manganoxydans
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_016618195.1 | GCA_016618195.1 |
Organism name | Providencia manganoxydans | Providencia manganoxydans |
Type category | type | type |
ANI | 98.81% | 98.81% |
Assembly coverage | 81.04% | 81.04% |
Type assembly coverage | 88.87% | 88.87% |
Chromosomes
Note: This scaffold-level genome assembly includes 104 scaffolds and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_041091175.1 | GCF_041091175.1 | ASM4109117v1 | Scaffold | Aug 7, 2024 |