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Source database (GenBank or RefSeq) File type

PDT000385584.1

Description:

NCBI Pathogen Detection Assembly PDT000385584.1

Organism name:

Salmonella enterica subsp. enterica serovar Enteritidis (enterobacteria)

Taxonomy check:

Infraspecific name:

Strain: CVM N17S949

BioSample:

SAMN10132960

BioProject:

PRJNA292661

Submitter:

FDA

Date:

2019/05/24

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_005767235.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

AADUCQ01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

68x

Sequencing technology:

ILLUMINA

IDs: 3156741 [UID] 10608858 [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_005767235.1	n/a	n/a	PDT000385584.1	Contig	Latest GenBank

Comment

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'.
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/  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##Annotation Date::09/27/2018 13:53:21
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Provider::NCBI
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Annotation Software revision::4.5
Genes (total)::4,841
CDS (total)::4,745
Genes (coding)::4,577
CDS (coding)::4,577
Genes (RNA)::96
rRNAs::3, 1, 3 (5S, 16S, 23S)
complete rRNAs::3 (5S)
partial rRNAs::1, 3 (16S, 23S)
tRNAs::74
ncRNAs::15
Pseudo Genes (total)::168
Pseudo Genes (ambiguous residues)::0 of 168
Pseudo Genes (frameshifted)::93 of 168
Pseudo Genes (incomplete)::73 of 168
Pseudo Genes (internal stop)::48 of 168
Pseudo Genes (multiple problems)::39 of 168
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	4,726,761
Total ungapped length	4,726,761
Number of contigs	28
Contig N50	489,863
Contig L50	3
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	28

	ANI	Query coverage	Subject coverage
Declared type	98.96	95.15	90.84
Best-match type	98.96	95.15	90.84

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Download Assembly

PDT000385584.1

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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Declared organism

Best-matching type-strain assembly for declared species

Best-matching type-strain assembly

Average Nucleotide Identity (ANI) data

ANI result