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ASM388653v1

Organism name:
Escherichia coli (E. coli)
Taxonomy check:
OK
Infraspecific name:
Strain: UMB3538
BioSample:
SAMN09665208
BioProject:
PRJNA316969
Submitter:
Loyola University Chicago
Date:
2018/12/06
Assembly type:
na
Assembly level:
Contig
Genome representation:
full
GenBank assembly accession:
GCA_003886535.1 (latest)
RefSeq assembly accession:
GCF_003886535.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
RRVB01
Assembly method:
SPAdes v. 3.11.1
Expected final version:
yes
Genome coverage:
80.67x
Sequencing technology:
Illumina MiSeq

IDs: 2140901 [UID] 8013438 [GenBank] 8067598 [RefSeq]

See Genome Information for Escherichia coli

There are 266030 assemblies for this organism

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History (Show revision history)

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/

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::12/01/2018 20:29:07
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::4.7
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::5,209
CDSs (total)::5,109
Genes (coding)::4,924
CDSs (with protein)::4,924
Genes (RNA)::100
rRNAs::6, 6, 2 (5S, 16S, 23S)
complete rRNAs::5, 1, 1 (5S, 16S, 23S)
partial rRNAs::1, 5, 1 (5S, 16S, 23S)
tRNAs::81
ncRNAs::5
Pseudo Genes (total)::185
CDSs (without protein)::185
Pseudo Genes (ambiguous residues)::0 of 185
Pseudo Genes (frameshifted)::87 of 185
Pseudo Genes (incomplete)::93 of 185
Pseudo Genes (internal stop)::40 of 185
Pseudo Genes (multiple problems)::33 of 185
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,152,159
Total ungapped length5,152,159
Number of contigs78
Contig N50173,830
Contig L5010
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)78

Supplemental Content

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Contig
Count
Ungapped
Length
Contig
N50
Spanned
Gaps
Unspanned
Gaps
unplaced5,152,159785,152,159173,83000

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Escherichia coliEscherichia coli

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_024519395.1Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775neotype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_024519395.1Escherichia colineotype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type99.9397.6494.10
Best-match type99.9397.6494.10

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna