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Source database (GenBank or RefSeq) File type

PDT001870758.1

Description:

NCBI Pathogen Detection Assembly PDT001870758.1

Organism name:

Escherichia coli (E. coli)

Taxonomy check:

Infraspecific name:

Strain: PF9V3-WW5_EC

BioSample:

SAMN37231926

BioProject:

PRJNA293225

Submitter:

US Food and Drug Administration

Date:

2023/09/04

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_031093085.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

ABLYDE01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

49x

Sequencing technology:

ILLUMINA

IDs: 18357861 [UID] 46880358 [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_031093085.1	n/a	n/a	PDT001870758.1	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::09/01/2023 23:41:40
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::2021-01-11.build5132
Genes (total)::4,727
CDSs (total)::4,633
Genes (coding)::4,462
CDSs (with protein)::4,462
Genes (RNA)::94
rRNAs::3, 1, 2 (5S, 16S, 23S)
complete rRNAs::3 (5S)
partial rRNAs::1, 2 (16S, 23S)
tRNAs::77
ncRNAs::11
Pseudo Genes (total)::171
CDSs (without protein)::171
Pseudo Genes (ambiguous residues)::0 of 171
Pseudo Genes (frameshifted)::67 of 171
Pseudo Genes (incomplete)::98 of 171
Pseudo Genes (internal stop)::51 of 171
Pseudo Genes (multiple problems)::41 of 171
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	4,869,748
Total ungapped length	4,869,748
Number of contigs	59
Contig N50	237,662
Contig L50	7
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	59

	ANI	Query coverage	Subject coverage
Declared type	99.59	92.16	85.16
Best-match type	99.59	92.16	85.16

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PDT001870758.1

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

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Average Nucleotide Identity (ANI) data

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