Genome assembly PDT000610242.1

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Submitted GenBank assembly
GCA_015638485.1
Taxon
Staphylococcus pseudintermedius
Strain
SPSE-19-VL-NY-FL-0019
WGS project
AAXKFT01
Submitter
Vet-LIRN-CVM-FDA
Date
Nov 20, 2020

Genome notes

NCBI has noted the following for this genome assembly. View definitions

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size2.7 Mb
Total ungapped length2.7 Mb
Number of contigs42
Contig N50255 kb
Contig L504
GC percent37.5
Genome coverage237.0x
Assembly levelContig

Sample details

BioSample ID
SAMN13049611
Description
Pathogen: environmental/food/other sample from Staphylococcus pseudintermedius
Submitter
FDA Center for Food Safety and Applied Nutrition
Isolation source
skin
Interagency Food Safety Analytics Collaboration (IFSAC) category
veterinary clinical/research| companion animal
Source type
animal
Collection date
May 17, 2019
Strain
SPSE-19-VL-NY-FL-0019
Attribute package
environmental/food/other
Isolate name alias
CFSAN100579
Collected by
Florida Department of Agriculture and Consumer Services; Bronson Animal Disease Diagnostic Laboratory
Geographic location
USA:FL
Ontological term
canis lupus familiaris:NCBITAXON_9615, zone of skin:UBERON_0000014
PublicAccession
CFSAN100579
ProjectAccession
PRJNA324567
Species
pseudintermedius
Genus
Staphylococcus
Host
Canis lupus familiaris
Host disease
Chronic otitis
Project name
Vet-LIRN
Sequenced by
WGS-NY
SRA
SRS5535336
CFSAN
CFSAN100579
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2019-10-17T13:31:06.560
Publication date
2019-10-17T00:00:00.000
Last updated
2024-12-20T10:02:17.350

Assembly methods

Sequencing technology
ILLUMINA
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/

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

Annotation details

GenBank
ProviderNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateOct 19, 2019
Genes2,579
Protein-coding2,438
Software version4.9

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.

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Quality 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 organismBest match type-strain
Type assemblyGCA_016026635.1GCA_016026635.1
Organism nameStaphylococcus pseudintermediusStaphylococcus pseudintermedius
Type categorytypetype
ANI99.49%99.49%
Assembly coverage90.21%90.21%
Type assembly coverage93.66%93.66%

Chromosomes

Note: This contig-level genome assembly includes 42 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_015638485.1

n/a

PDT000610242.1ContigNov 20, 2020