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Source database (GenBank or RefSeq) File type

PDT002112205.1

Description:

NCBI Pathogen Detection Assembly PDT002112205.1

Organism name:

Salmonella enterica (enterobacteria)

Taxonomy check:

Infraspecific name:

Strain: 24SC02GT05-S1

Isolate:

PNUSAS425664

BioSample:

SAMN40456041

BioProject:

PRJNA292661

Submitter:

FDA

Date:

2024/03/14

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_037161405.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

ABQRSV01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

64x

Sequencing technology:

ILLUMINA

IDs: 21864381 [UID] 54981118 [GenBank]

See Genome Information for Salmonella enterica

Pathogen Detection Resources

There are 527483 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_037161405.1	n/a	n/a	PDT002112205.1	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::03/14/2024 22:01:15
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)::4,704
CDSs (total)::4,607
Genes (coding)::4,525
CDSs (with protein)::4,525
Genes (RNA)::97
rRNAs::6, 2, 3 (5S, 16S, 23S)
complete rRNAs::6 (5S)
partial rRNAs::2, 3 (16S, 23S)
tRNAs::75
ncRNAs::11
Pseudo Genes (total)::82
CDSs (without protein)::82
Pseudo Genes (ambiguous residues)::0 of 82
Pseudo Genes (frameshifted)::38 of 82
Pseudo Genes (incomplete)::46 of 82
Pseudo Genes (internal stop)::19 of 82
Pseudo Genes (multiple problems)::19 of 82
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	4,833,997
Total ungapped length	4,833,997
Number of contigs	30
Contig N50	545,089
Contig L50	3
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	30

	ANI	Query coverage	Subject coverage
Declared type	98.50	88.89	88.24
Best-match type	98.50	88.89	88.24

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PDT002112205.1

See Genome Information for Salmonella enterica

Pathogen Detection Resources

There are 527483 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