Genome assembly PDT000484121.1

Actions
Submitted GenBank assembly
GCA_015605345.1
Taxon
Staphylococcus pseudintermedius
Strain
SPSE-18-VL-SD-IA-0033
WGS project
AAXJSD01
Submitter
Vet-LIRN-CVM-FDA
Date
Nov 19, 2020

Genome notes

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

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size2.5 Mb
Total ungapped length2.5 Mb
Number of contigs101
Contig N5046.5 kb
Contig L5016
GC percent37.5
Genome coverage156.0x
Assembly levelContig

Sample details

BioSample ID
SAMN11288846
Description
Pathogen: environmental/food/other sample from Staphylococcus pseudintermedius
Submitter
FDA Center for Food Safety and Applied Nutrition
Isolation source
skin (Canis lupus familiaris)
Interagency Food Safety Analytics Collaboration (IFSAC) category
veterinary clinical/research| companion animal
Source type
animal
Collection date
Sep 10, 2018
Strain
SPSE-18-VL-SD-IA-0033
Attribute package
environmental/food/other
Isolate name alias
CFSAN091779
Collected by
ISUVDL
Geographic location
USA:IA
Ontological term
canis lupus familiaris:NCBITAXON_9615, zone of skin:UBERON_0000014
PublicAccession
CFSAN091779
ProjectAccession
PRJNA318594
Species
pseudintermedius
Genus
Staphylococcus
SRA
SRS4556415
CFSAN
CFSAN091779
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2019-03-29T15:03:03.953
Publication date
2019-03-29T00:00:00.000
Last updated
2023-11-09T14:25:42.639

Assembly methods

Sequencing technology
ILLUMINA
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/

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)
DateMar 29, 2019
Genes2,414
Protein-coding2,279
Software version4.8

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

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_001792775.2GCA_001792775.2
Organism nameStaphylococcus pseudintermediusStaphylococcus pseudintermedius
Type categorytypetype
ANI99.46%99.46%
Assembly coverage93.56%93.56%
Type assembly coverage93.05%93.05%

Chromosomes

Note: This contig-level genome assembly includes 101 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_015605345.1

n/a

PDT000484121.1ContigNov 19, 2020