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ASM872679v1

Organism name:
Escherichia coli (E. coli)
Infraspecific name:
Strain: UMB1180
BioSample:
SAMN12797014
BioProject:
PRJNA316969
Submitter:
Loyola University Chicago
Date:
2019/09/28
Assembly type:
na
Assembly level:
Contig
Genome representation:
full
GenBank assembly accession:
GCA_008726795.1 (replaced)
RefSeq assembly accession:
GCF_008726795.1 (replaced)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
VYWI01
Assembly method:
SPAdes v. 3.11.1
Expected final version:
yes
Genome coverage:
44.96x
Sequencing technology:
Illumina MiSeq

IDs: 4743881 [UID] 14133288 [GenBank] 14256338 [RefSeq]

See Genome Information for Escherichia coli

There are 267822 assemblies for this organism

See more

History (Show revision history)

Comment

The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
This genome has been superseded by the updated assembly in the WGS project RRWD00000000

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::09/23/2019 20:52:02
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::4.9
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::4,604
CDSs (total)::4,504
Genes (coding)::4,377
CDSs (with protein)::4,377
Genes (RNA)::100
rRNAs::8, 2, 2 (5S, 16S, 23S)
complete rRNAs::6, 1, 1 (5S, 16S, 23S)
partial rRNAs::2, 1, 1 (5S, 16S, 23S)
tRNAs::79
ncRNAs::9
Pseudo Genes (total)::127
CDSs (without protein)::127
Pseudo Genes (ambiguous residues)::0 of 127
Pseudo Genes (frameshifted)::51 of 127
Pseudo Genes (incomplete)::77 of 127
Pseudo Genes (internal stop)::29 of 127
Pseudo Genes (multiple problems)::27 of 127
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length4,683,816
Total ungapped length4,683,816
Number of contigs88
Contig N50148,923
Contig L5010
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)88

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
unplaced4,683,816884,683,816148,92300

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_000010385.1Escherichia coli SE11claderef

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000010385.1Escherichia colicladeref

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type99.3193.6585.08
Best-match type99.3193.6585.08

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna