Genome assembly PDT002101104.1
- Submitted GenBank assembly
- GCA_037072305.1
- Taxon
- Staphylococcus pseudintermedius
- Strain
- SPSE-23-VL-SD-MI-0025
- WGS project
- ABQPNY01
- Submitter
- Vet-LIRN-CVM-FDA
- Date
- Mar 8, 2024
Genome notes
NCBI has noted the following for this genome assembly. View definitions
- from large multi-isolate project
Assembly statistics
GenBank | |
---|---|
Genome size | 2.6 Mb |
Total ungapped length | 2.6 Mb |
Number of contigs | 33 |
Contig N50 | 276.1 kb |
Contig L50 | 4 |
GC percent | 37.5 |
Genome coverage | 221.0x |
Assembly level | Contig |
Sample details
- BioSample ID
- SAMN40262492
- Description
- One Health Enteric sample from Staphylococcus pseudintermedius
- Submitter
- Vet-LIRN Project: SDSU Veterinary & Biomedical Sciences/ DOH South Dakota
- Strain
- SPSE-23-VL-SD-MI-0025
- Collected by
- Michigan State University Veterinary Diagnostic Laboratory
- Collection date
- Sep 30, 2023
- Geographic location
- USA:MI
- Isolation source
- Foot
- Source type
- animal
- Purpose of sampling
- Monitoring
- Host
- Canis lupus familiaris
- Host disease
- Pyoderma
- Project name
- Vet-LIRN
- Sequenced by
- South Dakota State University|South Dakota Animal Disease Research and Diagnostic Laboratory
- Sample name
- SPSE-23-VL-SD-MI-0025
- SRA
- SRS20691527
- Models
- One Health Enteric
- Package
- OneHealthEnteric.1.0
- Submission date
- 2024-03-05T10:45:07.987
- Publication date
- 2024-03-05T00:00:00.000
- Last updated
- 2024-03-07T16:53:40.797
Assembly methods
- Sequencing technology
- ILLUMINA
- Comment
The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/
This draft WGS assembly was generated by running SKESA to generate a de-novo assembly. The de-novo assembly was then concatenated with contigs generated using a guided assembler using antimicrobial resistance genes as baits to comprehensively catalog the set of resistance genes in the isolate. Note, some parts of the contigs derived from the guided assembler may overlap de-novo contigs, and other guided assembler contigs. De-novo contigs can be differentiated from guided assembler contigs by their names , which include either 'denovo' or 'guided'.
- Assembly method
- SKESA v. 2.2
Additional genomes
Browse all Staphylococcus pseudintermedius genomes (5353)BioProject
PRJNA318594Vet-LIRN-Staph-SD
Pathogen Detection Resource
Annotation details
GenBank | |
---|---|
Provider | NCBI |
Name | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Mar 8, 2024 |
Genes | 2,545 |
Protein-coding | 2,430 |
Software version | 2021-01-11.build5132 |
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
Taxonomy check
- Taxonomy check status
- OK
- Best match status
- species_match
- Submitted organism name
- Staphylococcus pseudintermedius
- Submitted species name
- Staphylococcus pseudintermedius
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_001792775.2 | GCA_001792775.2 |
Organism name | Staphylococcus pseudintermedius | Staphylococcus pseudintermedius |
Type category | type | type |
ANI | 99.5% | 99.5% |
Assembly coverage | 90.17% | 90.17% |
Type assembly coverage | 94.07% | 94.07% |
Chromosomes
Note: This contig-level genome assembly includes 33 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_037072305.1 | n/a | PDT002101104.1 | Contig | Mar 8, 2024 |