Genome assembly ASM152009v1

FTP
Actions
NCBI RefSeq assembly
GCF_001520095.1 (suppressed)
Submitted GenBank assembly
GCA_001520095.1
Taxon
Escherichia coli (E. coli)
Strain
GN02620
WGS project
LQUT01
Submitter
JCVI
Date
Jan 20, 2016

Genome notes

NCBI has noted the following for this genome assembly. View definitions

  • annotation fails completeness check

Assembly statistics

RefSeqGenBank
Genome size5 Mb5 Mb
Total ungapped length5 Mb5 Mb
Number of contigs303303
Contig N5034.4 kb34.4 kb
Contig L504646
GC percent5151
Genome coverage131.2x131.2x
Assembly levelContigContig
View sequencesview GenBank sequences

Sample details

BioSample ID
SAMN03922949
Description
Sample of Escherichia coli GN02620
Comment
Sample of Escherichia coli GN02620
Submitter
JCVI
Strain
GN02620
Collected by
Vance Fowler
Collection date
2007
Geographic location
USA
Host
Homo sapiens
Host disease
Bloodstream infection
Isolation source
bodily fluid
Latitude and longitude
36 N 78.9 W
Host health state
Diseased
SRA
SRS1246421
JCVI
GCID_ECOLID_00093
Models
Pathogen.cl
Package
Pathogen.cl.1.0
Submission date
2015-07-24T16:41:30.000
Publication date
2015-07-24T00:00:00.000
Last updated
2019-05-23T15:39:53.333

Assembly methods

Sequencing technology
Illumina NextSeq 500
Comment
Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
Assembly method
SPAdes v. 3.1.1

Additional genomes

Browse all Escherichia coli genomes (312327)

BioProject

PRJNA290784

Genomic sequencing of Escherichia coli bloodstream isolates

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateMay 23, 2023Jan 12, 2016
Genes5,2665,224
Protein-coding4,6834,762
Software version6.53.1

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: 95.48% (2nd Percentile)

Contamination: 0.89%

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
ANI99.89%99.89%
Assembly coverage97.43%97.43%
Type assembly coverage91.16%91.16%

Chromosomes

Note: This contig-level genome assembly includes 303 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_001520095.1GCF_001520095.1ASM152009v1ContigJan 20, 2016