Genome assembly ASM223285v1

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NCBI RefSeq assembly
GCF_002232855.1
Submitted GenBank assembly
GCA_002232855.1
Taxon
Escherichia coli (E. coli)
Strain
MOD1-EC5002
WGS project
NLUW01
Submitter
FDA/CFSAN
Date
Jul 25, 2017

Assembly statistics

RefSeqGenBank
Genome size5.4 Mb5.4 Mb
Total ungapped length5.4 Mb5.4 Mb
Number of contigs259259
Contig N50120.9 kb120.9 kb
Contig L501414
GC percent50.550.5
Genome coverage22.1x22.1x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN04279330
Description
Pathogen: clinical or host-associated sample from Escherichia coli
Submitter
CFSAN
Isolate name alias
99.0977
Strain
MOD1-EC5002
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 10, 1999
Geographic location
USA
Host
Homo sapiens
Collected by
Pennsylvania State University| Escherichia coli Reference Center
Food product origin geographic location
Singapore
Project name
GenomeTrakr
Sequenced by
Pennsylvania State University| Escherichia coli Reference Center
SRA
SRS1588654
CFSAN
CFSAN042090
Models
Pathogen.cl
Package
Pathogen.cl.1.0
Submission date
2015-11-19T13:36:21.000
Publication date
2015-11-19T00:00:00.000
Last updated
2024-08-08T11:36:11.998

Assembly methods

Sequencing technology
Illumina NextSeq 500
Assembly method
SPAdes v. 3.8.2

BioProject

PRJNA230969

GenomeTrakr Project: US Food and Drug Administration

Pathogen Detection Resource

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_002232855.1-RS_2024_04_29
DateApr 29, 2024
Genes5,413
Protein-coding5,031
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.

Continue reading

Quality analysis

CheckM analysis (v1.2.2)

Completeness: 99.47% (89th Percentile)

Contamination: 0.71%

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_000350825.1GCA_000350825.1
Organism nameEscherichia coli KTE26Escherichia coli
Type categorycladerefcladeref
ANI98.3%98.3%
Assembly coverage84.95%84.95%
Type assembly coverage86.38%86.38%

Chromosomes

Note: This contig-level genome assembly includes 259 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002232855.1GCF_002232855.1ASM223285v1ContigJul 25, 2017