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Source database (GenBank or RefSeq) File type

PDT000688605.1

Description:

NCBI Pathogen Detection Assembly PDT000688605.1

Organism name:

Escherichia coli (E. coli)

Taxonomy check:

Infraspecific name:

Strain: USECESBL182

BioSample:

SAMN14146644

BioProject:

PRJNA293225

Submitter:

US Food and Drug Administration

Date:

2020/04/23

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_012697585.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

AATBHH01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

97x

Sequencing technology:

ILLUMINA

IDs: 6929931 [UID] 19109428 [GenBank]

See Genome Information for Escherichia coli

Pathogen Detection Resources

There are 266204 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_012697585.1	n/a	n/a	PDT000688605.1	Contig	Latest GenBank

Comment

The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/
This draft WGS assembly was generated by running SKESA to generate a de-novo assembly. The ... de-novo assembly was then concatenated with contigs generated using a guided assembler using antimicrobial resistance genes as baits to comprehensively catalog the set of resistance genes in the isolate. Note, some parts of the contigs derived from the guided assembler may overlap de-novo contigs, and other guided assembler contigs. De-novo contigs can be differentiated from guided assembler contigs by their names , which include either 'denovo' or 'guided'.  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##Annotation Date::02/26/2020 04:52:41
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Provider::NCBI
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Annotation Software revision::2020-02-06.build4373
Genes (total)::4,593
CDSs (total)::4,495
Genes (coding)::4,372
CDSs (with protein)::4,372
Genes (RNA)::98
rRNAs::7, 3, 2 (5S, 16S, 23S)
complete rRNAs::2 (5S)
partial rRNAs::5, 3, 2 (5S, 16S, 23S)
tRNAs::76
ncRNAs::10
Pseudo Genes (total)::123
CDSs (without protein)::123
Pseudo Genes (ambiguous residues)::0 of 123
Pseudo Genes (frameshifted)::41 of 123
Pseudo Genes (incomplete)::66 of 123
Pseudo Genes (internal stop)::26 of 123
Pseudo Genes (multiple problems)::10 of 123
CRISPR Arrays::1
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	4,685,568
Total ungapped length	4,685,568
Number of contigs	90
Contig N50	147,774
Contig L50	11
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	90

	ANI	Query coverage	Subject coverage
Declared type	99.41	90.89	79.95
Best-match type	99.41	90.89	79.95

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PDT000688605.1

See Genome Information for Escherichia coli

Pathogen Detection Resources

There are 266204 assemblies for this organism

History (Show revision history)

Comment

Genome-Annotation-Data

Global statistics

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Declared organism

Best-matching type-strain assembly for declared species

Best-matching type-strain assembly

Average Nucleotide Identity (ANI) data

ANI result