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Source database (GenBank or RefSeq) File type

PDT000495569.1

Description:

NCBI Pathogen Detection Assembly PDT000495569.1

Organism name:

Salmonella enterica (enterobacteria)

Taxonomy check:

Infraspecific name:

Strain: 19WA02CB38-S1

BioSample:

SAMN11510001

BioProject:

PRJNA292661

Submitter:

FDA

Date:

2019/05/20

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_005512815.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

AADBRT01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

86x

Sequencing technology:

ILLUMINA

IDs: 2935731 [UID] 10129628 [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_005512815.1	n/a	n/a	PDT000495569.1	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::04/25/2019 18:28:19
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Provider::NCBI
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Annotation Software revision::4.8
Genes (total)::4,987
CDSs (total)::4,881
Genes (coding)::4,714
CDSs (with protein)::4,714
Genes (RNA)::106
rRNAs::6, 4, 6 (5S, 16S, 23S)
complete rRNAs::6 (5S)
partial rRNAs::4, 6 (16S, 23S)
tRNAs::76
ncRNAs::14
Pseudo Genes (total)::167
CDSs (without protein)::167
Pseudo Genes (ambiguous residues)::0 of 167
Pseudo Genes (frameshifted)::81 of 167
Pseudo Genes (incomplete)::90 of 167
Pseudo Genes (internal stop)::52 of 167
Pseudo Genes (multiple problems)::50 of 167
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	4,985,165
Total ungapped length	4,985,165
Number of contigs	156
Contig N50	70,412
Contig L50	23
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	156

	ANI	Query coverage	Subject coverage
Declared type	98.73	88.10	90.41
Best-match type	98.73	88.10	90.41

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PDT000495569.1

See Genome Information for Salmonella enterica

Pathogen Detection Resources

There are 527483 assemblies for this organism

History (Show revision history)

Comment

Genome-Annotation-Data

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Best-matching type-strain assembly for declared species

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Average Nucleotide Identity (ANI) data

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