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Source database (GenBank or RefSeq) File type

PDT001856726.1

Description:

NCBI Pathogen Detection Assembly PDT001856726.1

Organism name:

Salmonella enterica (enterobacteria)

Taxonomy check:

Infraspecific name:

Strain: 23NC07CH01-S

BioSample:

SAMN37073119

BioProject:

PRJNA292661

Submitter:

FDA

Date:

2023/09/18

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_031615335.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

ABMNFX01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

46x

Sequencing technology:

ILLUMINA

IDs: 18627191 [UID] 47596278 [GenBank]

See Genome Information for Salmonella enterica

Pathogen Detection Resources

There are 527347 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_031615335.1	n/a	n/a	PDT001856726.1	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::08/21/2023 18:13:35
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)::4,780
CDSs (total)::4,678
Genes (coding)::4,561
CDSs (with protein)::4,561
Genes (RNA)::102
rRNAs::5, 3, 6 (5S, 16S, 23S)
complete rRNAs::5 (5S)
partial rRNAs::3, 6 (16S, 23S)
tRNAs::74
ncRNAs::14
Pseudo Genes (total)::117
CDSs (without protein)::117
Pseudo Genes (ambiguous residues)::0 of 117
Pseudo Genes (frameshifted)::54 of 117
Pseudo Genes (incomplete)::73 of 117
Pseudo Genes (internal stop)::29 of 117
Pseudo Genes (multiple problems)::35 of 117
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	4,919,601
Total ungapped length	4,919,601
Number of contigs	95
Contig N50	110,502
Contig L50	16
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	95

	ANI	Query coverage	Subject coverage
Declared type	98.73	89.24	90.38
Best-match type	98.73	89.24	90.38

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Download Assembly

PDT001856726.1

See Genome Information for Salmonella enterica

Pathogen Detection Resources

There are 527347 assemblies for this organism

History (Show revision history)

Comment

Genome-Annotation-Data

Global statistics

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Taxonomy Check Data

Declared organism

Best-matching type-strain assembly for declared species

Best-matching type-strain assembly

Average Nucleotide Identity (ANI) data

ANI result