Genome assembly PDT000501714.2

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Submitted GenBank assembly
GCA_020312535.1
Taxon
Escherichia coli (E. coli)
Strain
CFSAN084809
WGS project
ABCYNK01
Submitter
FDA/CFSAN
Date
Oct 6, 2021

Genome notes

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

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size5.4 Mb
Total ungapped length5.4 Mb
Number of contigs214
Contig N5056.3 kb
Contig L5029
GC percent50.5
Genome coverage119.0x
Assembly levelContig

Sample details

BioSample ID
SAMN11658288
Description
Pathogen: environmental/food/other sample from Escherichia coli
Submitter
FDA Center for Food Safety and Applied Nutrition
Isolation source
cattle manure
Interagency Food Safety Analytics Collaboration (IFSAC) category
environmental| cow
Source type
environmental
Collection date
Mar 26, 2018
Strain
CFSAN084809
Attribute package
environmental/food/other
Isolate name alias
MJ-2015-1
Collected by
Western Center for Food Safety
Geographic location
USA
Ontological term
animal manure:ENVO_00003031, bos taurus:NCBITAXON_9913, cattle:FOODON_03411161
PublicAccession
CFSAN084809
ProjectAccession
PRJNA230969
Species
coli
Genus
Escherichia
Project name
GenomeTrakr
Sequenced by
United States Food and Drug Administration| Center for Food Safety and Applied Nutrition
Food product origin geographic location
USA:AZ
Host
Bos taurus
SRA
SRS4768634
CFSAN
CFSAN084809
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2019-05-16T06:41:04.510
Publication date
2019-05-16T00:00:00.000
Last updated
2024-08-08T11:46:15.330

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 (311553)

BioProject

PRJNA230969

GenomeTrakr Project: US Food and Drug Administration

Pathogen Detection Resource

Annotation details

GenBank
ProviderNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateOct 2, 2021
Genes5,472
Protein-coding5,144
Software version2021-01-11.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.

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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_000210475.1GCA_000210475.1
Organism nameEscherichia coli ETEC H10407Escherichia coli
Type categorycladerefcladeref
ANI98.76%98.76%
Assembly coverage81.13%81.13%
Type assembly coverage82.36%82.36%

Chromosomes

Note: This contig-level genome assembly includes 214 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_020312535.1

n/a

PDT000501714.2ContigOct 6, 2021