Genome assembly ASM222829v1

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NCBI RefSeq assembly
GCF_002228295.1
Submitted GenBank assembly
GCA_002228295.1
Taxon
Escherichia coli (E. coli)
Strain
MOD1-EC5567
WGS project
NLLG01
Submitter
FDA/CFSAN
Date
Jul 25, 2017

Assembly statistics

RefSeqGenBank
Genome size5.2 Mb5.2 Mb
Total ungapped length5.2 Mb5.2 Mb
Number of contigs371371
Contig N5052.9 kb52.9 kb
Contig L502727
GC percent50.550.5
Genome coverage97.3x97.3x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN05440372
Description
Pathogen: environmental/food/other sample from Escherichia coli
Submitter
FDA Center for Food Safety and Applied Nutrition
Isolate name alias
CFSAN049813,C-B-09-2-2-M-10
Strain
MOD1-EC5567
Attribute package
environmental/food/other
Isolation source
chicken feces
Ontological term
chicken:FOODON_03411457| feces:UBERON_0001988| gallus gallus:NCBITAXON_9031
Interagency Food Safety Analytics Collaboration (IFSAC) category
veterinary clinical/research| chicken
Source type
animal
Collection date
Apr 24, 1979
Geographic location
USA
Host
Gallus gallus
Collected by
Pennsylvania State University| Escherichia coli Reference Center
Food product origin geographic location
USA:CO
Project name
GenomeTrakr
Sequenced by
Pennsylvania State University| Escherichia coli Reference Center
SRA
SRS1594172
CFSAN
CFSAN049813
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2016-07-26T09:11:15.613
Publication date
2016-07-26T00:00:00.000
Last updated
2024-08-08T11:39:09.071

Assembly methods

Sequencing technology
Illumina NextSeq 500
Assembly method
SPAdes v. 3.8.2

Additional genomes

Browse all Escherichia coli genomes (311553)

BioProject

PRJNA230969

GenomeTrakr Project: US Food and Drug Administration

Pathogen Detection Resource

Annotation details

RefSeq
ProviderNCBI RefSeq
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateFeb 4, 2024
Genes5,455
Protein-coding5,022
Software version6.6

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

CheckM analysis (v1.2.2)

Completeness: 97.46% (7th Percentile)

Contamination: 0.39%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Escherichia coli CheckM marker set. For more information on CheckM, see Parks, et al. Genome Res (2015).

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
ANI98.98%98.98%
Assembly coverage84.52%84.52%
Type assembly coverage83%83%

Chromosomes

Note: This contig-level genome assembly includes 371 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002228295.1GCF_002228295.1ASM222829v1ContigJul 25, 2017