Genome assembly ASM4109117v1

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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

RefSeqGenBank
Genome size4.8 Mb4.8 Mb
Total ungapped length4.8 Mb4.8 Mb
Number of scaffolds104104
Scaffold N50177.1 kb177.1 kb
Scaffold L5099
Number of contigs115115
Contig N50149 kb149 kb
Contig L501111
GC percent40.540.5
Genome coverage200.0x200.0x
Assembly levelScaffoldScaffold
View sequencesview 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

PRJNA1093566

Role of Flies in the Dissemination of Carbapenem-Resistant Enterobacteriaceae (CRE): An Epidemiological and Genomic Study in China

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_041091175.1-RS_2024_08_08NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateAug 8, 2024Aug 2, 2024
Genes4,4894,488
Protein-coding4,3114,327
Software version6.76.7

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 reading

Quality 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 organismBest match type-strain
Type assemblyGCA_016618195.1GCA_016618195.1
Organism nameProvidencia manganoxydansProvidencia manganoxydans
Type categorytypetype
ANI98.81%98.81%
Assembly coverage81.04%81.04%
Type assembly coverage88.87%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_041091175.1GCF_041091175.1ASM4109117v1ScaffoldAug 7, 2024