Genome assembly PDT000246493.2

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Submitted GenBank assembly
GCA_012384175.1
Taxon
Escherichia coli (E. coli)
Strain
ECOL-17-VL-NY-GA-0017
WGS project
AASJIN01
Submitter
Vet-LIRN-CVM-FDA
Date
Apr 15, 2020

Genome notes

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

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size5.1 Mb
Total ungapped length5.1 Mb
Number of contigs97
Contig N50131.3 kb
Contig L5014
GC percent50.5
Genome coverage57.0x
Assembly levelContig

Sample details

BioSample ID
SAMN07709810
Description
Pathogen: environmental/food/other sample from Escherichia coli
Submitter
FDA Center for Food Safety and Applied Nutrition
Isolation source
urine
Interagency Food Safety Analytics Collaboration (IFSAC) category
veterinary clinical/research| companion animal
Source type
animal
Collection date
Jun 20, 2017
Strain
ECOL-17-VL-NY-GA-0017
Attribute package
environmental/food/other
Isolate name alias
CFSAN069801
Collected by
University of Georgia College of Veterinary Medicine Tifton Veterinary Diagnostic and Investigational Laboratory
Geographic location
USA:GA
Ontological term
dog:FOODON_03414847, urine:UBERON_0001088
PublicAccession
CFSAN069801
ProjectAccession
PRJNA324565
Species
coli
Genus
Escherichia
Host
Canis lupus familiaris
Project name
Vet-LIRN
Sequenced by
WGS-NY
SRA
SRS2555656
CFSAN
CFSAN069801
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2017-09-27T10:31:06.803
Publication date
2017-09-27T00:00:00.000
Last updated
2024-12-20T10:02:06.874

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 Escherichia coli genomes (311916)

BioProject

PRJNA324565

Vet-LIRN-E.coli-NY

Pathogen Detection Resource

Annotation details

GenBank
ProviderNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateMar 13, 2020
Genes4,903
Protein-coding4,679
Software version2020-02-06.build4373

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
Escherichia coli
Submitted species name
Escherichia coli

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_000013265.1GCA_000013265.1
Organism nameEscherichia coli UTI89Escherichia coli
Type categorycladerefcladeref
ANI99.05%99.05%
Assembly coverage90.81%90.81%
Type assembly coverage89.39%89.39%

Chromosomes

Note: This contig-level genome assembly includes 97 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_012384175.1

n/a

PDT000246493.2ContigApr 15, 2020