Genome assembly ASM248656v1

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NCBI RefSeq assembly
GCF_002486565.1
Submitted GenBank assembly
GCA_002486565.1
Taxon
Escherichia coli (E. coli)
Strain
MOD1-EC4366
WGS project
NWNO01
Submitter
FDA/CFSAN
Date
Oct 6, 2017

Assembly statistics

RefSeqGenBank
Genome size5.3 Mb5.3 Mb
Total ungapped length5.3 Mb5.3 Mb
Number of contigs278278
Contig N50148.5 kb148.5 kb
Contig L501010
GC percent50.550.5
Genome coverage72.0x72.0x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN04913996
Description
Pathogen: environmental/food/other sample from Escherichia coli
Submitter
FDA Center for Food Safety and Applied Nutrition
Attribute package
environmental/food/other
Isolation source
environment
Ontological term
environmental system:envo_01000254
Interagency Food Safety Analytics Collaboration (IFSAC) category
environmental
Source type
environmental
Collection date
Oct 26, 2006
Geographic location
USA
Isolate name alias
RM5687; CFSAN039062
Strain
MOD1-EC4366
Collected by
United States Food and Drug Administration
Food product origin geographic location
USA:CA
Project name
GenomeTrakr
Sequenced by
United States Food and Drug Administration| Center for Food Safety and Applied Nutrition
SRA
SRS1584425
CFSAN
CFSAN039062
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2016-04-28T15:51:10.000
Publication date
2016-04-28T00:00:00.000
Last updated
2024-08-08T11:37:54.994

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
NameGCF_002486565.1-RS_2024_07_02
DateJul 2, 2024
Genes5,462
Protein-coding5,016
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 (v1.2.3)

Completeness: 99.37% (81st Percentile)

Contamination: 0.15%

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_001281725.1GCA_001281725.1
Organism nameEscherichia coliEscherichia coli
Type categorycladerefcladeref
ANI99.92%99.92%
Assembly coverage96.98%96.98%
Type assembly coverage96.86%96.86%

Chromosomes

Note: This contig-level genome assembly includes 278 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002486565.1GCF_002486565.1ASM248656v1ContigOct 6, 2017