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ASM388505v1

Organism name:
Escherichia coli (E. coli)
Taxonomy check:
OK
Infraspecific name:
Strain: UMB1221
BioSample:
SAMN10411422
BioProject:
PRJNA316969
Submitter:
Loyola University Chicago
Date:
2018/12/06
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_003885055.1 (latest)
RefSeq assembly accession:
GCF_003885055.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
RRUG01
Assembly method:
SPAdes v. 3.11.1
Expected final version:
yes
Genome coverage:
91.6x
Sequencing technology:
Illumina MiSeq

IDs: 2140131 [UID] 8011978 [GenBank] 8066598 [RefSeq]

See Genome Information for Escherichia coli

There are 267915 assemblies for this organism

See more

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 19:48:57
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)::5,359
CDSs (total)::5,262
Genes (coding)::5,046
CDSs (with protein)::5,046
Genes (RNA)::97
rRNAs::7, 3, 1 (5S, 16S, 23S)
complete rRNAs::6, 1 (5S, 23S)
partial rRNAs::1, 3 (5S, 16S)
tRNAs::80
ncRNAs::6
Pseudo Genes (total)::216
CDSs (without protein)::216
Pseudo Genes (ambiguous residues)::1 of 216
Pseudo Genes (frameshifted)::115 of 216
Pseudo Genes (incomplete)::103 of 216
Pseudo Genes (internal stop)::37 of 216
Pseudo Genes (multiple problems)::37 of 216
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,320,813
Total ungapped length5,320,520
Gaps between scaffolds0
Number of scaffolds64
Scaffold N50322,151
Scaffold L506
Number of contigs67
Contig N50322,151
Contig L506
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)64

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
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced5,320,813645,320,520322,15130

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_000013265.1Escherichia coli UTI89claderef

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000013265.1Escherichia colicladeref

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type98.9687.6189.99
Best-match type98.9687.6189.99

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna