Genome assembly ASM253773v1

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NCBI RefSeq assembly
GCF_002537735.1
Submitted GenBank assembly
GCA_002537735.1
Taxon
Escherichia coli (E. coli)
Strain
MOD1-EC6054
WGS project
NMDT01
Submitter
FDA/CFSAN
Date
Oct 13, 2017

Assembly statistics

RefSeqGenBank
Genome size5 Mb5 Mb
Total ungapped length5 Mb5 Mb
Number of contigs7070
Contig N50232.6 kb232.6 kb
Contig L5088
GC percent50.550.5
Genome coverage53.6x53.6x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN05439501
Description
Pathogen: environmental/food/other sample from Escherichia coli
Submitter
FDA Center for Food Safety and Applied Nutrition
Isolate name alias
CFSAN044291, 104
Strain
MOD1-EC6054
Attribute package
clinical/host-associated
Isolation source
feces
Ontological term
feces:uberon_0001988
Interagency Food Safety Analytics Collaboration (IFSAC) category
clinical/research| human
Source type
human
Collection date
Jun 30, 2010
Geographic location
USA
Host
Homo sapiens
Collected by
Pennsylvania State University| Escherichia coli Reference Center
Food product origin geographic location
Norway
Project name
GenomeTrakr
Sequenced by
Pennsylvania State University| Escherichia coli Reference Center
SRA
SRS1593192
CFSAN
CFSAN044291
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2016-07-25T16:57:29.133
Publication date
2016-07-25T00:00:00.000
Last updated
2024-08-08T11:39:05.019

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

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_002537735.1-RS_2024_12_01
DateDec 1, 2024
Genes4,892
Protein-coding4,626
Software version6.9

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 (v1.2.3)

Completeness: 99.18% (65th Percentile)

Contamination: 0.5%

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_000013265.1GCA_000013265.1
Organism nameEscherichia coli UTI89Escherichia coli
Type categorycladerefcladeref
ANI98.91%98.91%
Assembly coverage90.49%90.49%
Type assembly coverage87.02%87.02%

Chromosomes

Note: This contig-level genome assembly includes 70 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002537735.1GCF_002537735.1ASM253773v1ContigOct 13, 2017