Genome assembly ASM246629v1

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NCBI RefSeq assembly
GCF_002466295.1
Submitted GenBank assembly
GCA_002466295.1
Taxon
Escherichia coli (E. coli)
Strain
MOD1-EC329
WGS project
NJMB01
Submitter
FDA/CFSAN
Date
Oct 6, 2017

Assembly statistics

RefSeqGenBank
Genome size5 Mb5 Mb
Total ungapped length5 Mb5 Mb
Number of contigs261261
Contig N5075.4 kb75.4 kb
Contig L502121
GC percent50.550.5
Genome coverage60.0x60.0x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN05591591
Description
Pathogen: environmental/food/other sample from Escherichia coli
Submitter
FDA Center for Food Safety and Applied Nutrition
Collected by
University of Iowa
Strain
MOD1-EC329
Collection date
2006
Isolate name alias
CFSAN054144, E2531
Attribute package
clinical/host-associated
Ontological term
missing:GENEPIO_0001618
Interagency Food Safety Analytics Collaboration (IFSAC) category
clinical/research
Source type
Unknown
CFSAN
CFSAN054144
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2016-08-18T15:22:15.070
Publication date
2016-08-18T00:00:00.000
Last updated
2020-11-05T13:29:35.952

Assembly methods

Sequencing technology
Illumina NextSeq 500
Assembly method
SPAdes v. 3.8.2

Additional genomes

Browse all Escherichia coli genomes (312111)

BioProject

PRJNA230969

GenomeTrakr Project: US Food and Drug Administration

Pathogen Detection Resource

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_002466295.1-RS_2024_04_25
DateApr 25, 2024
Genes5,207
Protein-coding4,780
Software version6.7

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

CheckM analysis (v1.2.2)

Completeness: 99.21% (68th Percentile)

Contamination: 0.25%

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
ANI99.53%99.53%
Assembly coverage88.65%88.65%
Type assembly coverage83.98%83.98%

Chromosomes

Note: This contig-level genome assembly includes 261 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002466295.1GCF_002466295.1ASM246629v1ContigOct 6, 2017