Genome assembly ASM296529v1

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NCBI RefSeq assembly
GCF_002965295.1
Submitted GenBank assembly
GCA_002965295.1
Taxon
Escherichia sp. MOD1-EC5949
Strain
MOD1-EC5949
WGS project
PTSS01
Submitter
FDA/CFSAN
Date
Feb 28, 2018

Assembly statistics

RefSeqGenBank
Genome size4.7 Mb4.7 Mb
Total ungapped length4.7 Mb4.7 Mb
Number of contigs127127
Contig N50151.2 kb151.2 kb
Contig L501010
GC percent50.550.5
Genome coverage28.7x28.7x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN05439388
Description
Pathogen: environmental/food/other sample from Escherichia sp.
Submitter
FDA Center for Food Safety and Applied Nutrition
Isolation source
feces
Collected by
Penn State E. coli Reference Center
Strain
MOD1-EC5949
Geographic location
USA:AK
Collection date
Jul 30, 2008
Isolate name alias
CFSAN044186, 807160033
Attribute package
clinical/host-associated
Host
Anas platyrhynchos
Genotype
cryptic lineage 5
SRA
SRS1592793
CFSAN
CFSAN044186
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2016-07-25T16:42:03.916
Publication date
2016-07-25T00:00:00.000
Last updated
2021-02-10T11:21:37.949

Assembly methods

Sequencing technology
Illumina NextSeq 500
Assembly method
SPAdes v. 3.8.2

Additional genomes

Browse all Escherichia sp. MOD1-EC5949 genomes (1)

BioProject

PRJNA230969

GenomeTrakr Project: US Food and Drug Administration

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_002965295.1-RS_2024_03_14
DateMar 14, 2024
Genes4,724
Protein-coding4,422
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: 95.79% (100th Percentile)

Contamination: 0.1%

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

Taxonomy check

Taxonomy check status
OK
Best match status
genus_match
Submitted organism name
Escherichia sp. MOD1_EC5949
Submitted species name
Escherichia sp. MOD1_EC5949

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assembly

n/a

GCA_002900365.1
Organism name

n/a

Escherichia marmotae
Type category

n/a

type
ANI

n/a

99.31%
Assembly coverage

n/a

84.35%
Type assembly coverage

n/a

81.36%

Chromosomes

Note: This contig-level genome assembly includes 127 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002965295.1GCF_002965295.1ASM296529v1ContigFeb 28, 2018