Genome assembly PDT002466010.1

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Submitted GenBank assembly
GCA_044905865.1
Taxon
Escherichia coli UTI89
Strain
ECOL-24-VL-NY-FL-0009
WGS project
ABWJLH01
Submitter
Vet-LIRN-CVM-FDA
Date
Nov 14, 2024

Genome notes

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

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size5.2 Mb
Total ungapped length5.2 Mb
Number of contigs50
Contig N50540.3 kb
Contig L504
GC percent50.5
Genome coverage177.0x
Assembly levelContig

Sample details

BioSample ID
SAMN44733941
Description
One Health Enteric sample from Escherichia coli UTI89
Submitter
Vet-LIRN: Cornell University, Ithaca, NY
Strain
ECOL-24-VL-NY-FL-0009
Collected by
Florida Department of Agriculture and Consumer Services; Bronson Animal Disease Diagnostic Laboratory
Collection date
Apr 16, 2024
Geographic location
USA:FL
Isolation source
urine
Source type
animal
Purpose of sampling
Monitoring (AMR project)
Host
Canis lupus familiaris
Host disease
Infection
Intended consumer
not applicable
Project name
Vet-LIRN
Sequenced by
WGS-NY
Sample name
ECOL-24-VL-NY-FL-0009
SRA
SRS23214111
Models
One Health Enteric
Package
OneHealthEnteric.1.0
Submission date
2024-11-14T07:17:04.600
Publication date
2024-11-14T00:00:00.000
Last updated
2024-11-14T07:24:28.270

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 (311944)

BioProject

PRJNA324565

Vet-LIRN-E.coli-NY

Pathogen Detection Resource

Annotation details

GenBank
ProviderNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateNov 14, 2024
Genes5,069
Protein-coding4,761
Software version2024-07-18.build7555

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
Escherichia coli UTI89
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
ANI99.08%99.08%
Assembly coverage88.79%88.79%
Type assembly coverage88.95%88.95%

Chromosomes

Note: This contig-level genome assembly includes 50 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_044905865.1

n/a

PDT002466010.1ContigNov 14, 2024