Genome assembly ASM623426v1

Actions
NCBI RefSeq assembly
GCF_006234265.1
Submitted GenBank assembly
GCA_006234265.1
Taxon
Escherichia coli (E. coli)
Strain
NOR2_60
WGS project
SQFY01
Submitter
University of Tartu
Date
Jun 11, 2019

Assembly statistics

RefSeqGenBank
Genome size5.1 Mb5.1 Mb
Total ungapped length5.1 Mb5.1 Mb
Number of scaffolds105105
Scaffold N50266.5 kb266.5 kb
Scaffold L5077
Number of contigs226226
Contig N5081.2 kb81.2 kb
Contig L502121
GC percent5151
Genome coverage83.1x83.1x
Assembly levelScaffoldScaffold

Sample details

BioSample ID
SAMN11232906
Description
Pathogen: clinical or host-associated sample from Escherichia coli
Submitter
University of Tartu
Strain
NOR2_60
Collected by
Baltic ESBL Project
Collection date
2012
Geographic location
Norway
Host
Homo sapiens
Isolation source
clinical sample
Sample name
NOR2_60
Models
Pathogen.cl
Package
Pathogen.cl.1.0
Submission date
2019-03-22T09:33:17.290
Publication date
2019-03-22T00:00:00.000
Last updated
2019-03-22T09:33:17.290

Assembly methods

Sequencing technology
HiSeq2500 Rapid Run
Assembly method
Velvet v. 1.2.10

Additional genomes

Browse all Escherichia coli genomes (311553)

BioProject

PRJNA528606

Escherichia coli Genome sequencing and assembly

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_006234265.1-RS_2024_07_09
DateJul 9, 2024
Genes5,127
Protein-coding4,823
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: 99.02% (54th Percentile)

Contamination: 0.75%

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_024519395.1GCA_024519395.1
Organism nameEscherichia coli DSM 30083 = JCM 1649 = ATCC 11775Escherichia coli
Type categoryneotypeneotype
ANI99.9%99.9%
Assembly coverage98.27%98.27%
Type assembly coverage93.91%93.91%

Chromosomes

Note: This scaffold-level genome assembly includes 105 scaffolds and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_006234265.1GCF_006234265.1ASM623426v1ScaffoldJun 11, 2019