Genome assembly 17870_6#13

Actions
Taxon
Escherichia coli (E. coli)
Strain
VRES0580
WGS project
UDEX01
Submitter
SC
Date
Jun 30, 2018

Assembly statistics

RefSeqGenBank
Genome size5.2 Mb5.2 Mb
Total ungapped length5.2 Mb5.2 Mb
Number of scaffolds6060
Scaffold N50402.1 kb402.1 kb
Scaffold L5055
Number of contigs6565
Contig N50331.9 kb331.9 kb
Contig L5066
GC percent50.550.5
Genome coverage100.0x100.0x
Assembly levelScaffoldScaffold

Sample details

BioSample ID
SAMEA3752319
Description
17870_6#13
Submitter
EBI
ENA last update
Jul 1, 2015
ENA-CHECKLIST
ERC000011
ENA-FIRST-PUBLIC
2016-01-12T09:05:50Z
ENA-LAST-UPDATE
2018-03-09T13:36:50Z
External Id
SAMEA3752319
INSDC center name
SC
INSDC first public
2016-01-12T09:05:50Z
INSDC last update
2018-03-09T13:36:50Z
INSDC status
public
Submitter Id
VRES0580-sc-2341060
Collection date
2015
Geographic location
United Kingdom
Host health state
carriage
Isolation source
feces
Sample name
VRES0580-sc-2341060
Scientific name
Escherichia coli
Host
Meleagris gallopavo
Strain
VRES0580
Supplier name
VRES0580
SRA
ERS784640
Models
Generic
Package
Generic.1.0
Submission date
2016-01-13T08:11:34.673
Publication date
2016-01-12T00:00:00.000
Last updated
2024-02-06T09:24:12.000

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqSC
NameGCF_900481605.1-RS_2024_06_16Annotation submitted by SC
DateJun 16, 2024Jun 30, 2018
Genes5,1294,907
Protein-coding4,7814,813
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: 99.1% (59th Percentile)

Contamination: 1.03%

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_002853715.1GCA_002853715.1
Organism nameEscherichia coliEscherichia coli
Type categorycladerefcladeref
ANI99.8%99.8%
Assembly coverage92.2%92.2%
Type assembly coverage93.01%93.01%

Chromosomes

Note: This scaffold-level genome assembly includes 60 scaffolds and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_900481605.1GCF_900481605.117870_6#13ScaffoldJun 30, 2018