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Source database (GenBank or RefSeq) File type

PDT000579128.1

Description:

NCBI Pathogen Detection Assembly PDT000579128.1

Organism name:

Salmonella enterica subsp. enterica serovar Infantis (enterobacteria)

Taxonomy check:

Infraspecific name:

Strain: 19MD07GT06-S

BioSample:

SAMN12684373

BioProject:

PRJNA292661

Submitter:

FDA

Date:

2019/09/06

Assembly type:

Assembly level:

Contig

Genome representation:

full

Excluded from RefSeq:

from large multi-isolate project

GenBank assembly accession:

GCA_008298325.1 (latest)

RefSeq assembly accession:

n/a

RefSeq assembly and GenBank assembly identical:

n/a

WGS Project:

AAKCTU01

Assembly method:

SKESA v. 2.2

Expected final version:

Genome coverage:

49x

Sequencing technology:

ILLUMINA

IDs: 4532481 [UID] 13633968 [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_008298325.1	n/a	n/a	PDT000579128.1	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'.
The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##Annotation Date::09/03/2019 18:29:46
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::4.9
Genes (total)::5,027
CDSs (total)::4,925
Genes (coding)::4,743
CDSs (with protein)::4,743
Genes (RNA)::102
rRNAs::8, 3, 4 (5S, 16S, 23S)
complete rRNAs::6 (5S)
partial rRNAs::2, 3, 4 (5S, 16S, 23S)
tRNAs::74
ncRNAs::13
Pseudo Genes (total)::182
CDSs (without protein)::182
Pseudo Genes (ambiguous residues)::0 of 182
Pseudo Genes (frameshifted)::74 of 182
Pseudo Genes (incomplete)::124 of 182
Pseudo Genes (internal stop)::51 of 182
Pseudo Genes (multiple problems)::53 of 182
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	5,034,194
Total ungapped length	5,034,194
Number of contigs	73
Contig N50	191,713
Contig L50	8
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	73

	ANI	Query coverage	Subject coverage
Declared type	98.90	87.78	90.29
Best-match type	98.90	87.78	90.29

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PDT000579128.1

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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Declared organism

Best-matching type-strain assembly for declared species

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Average Nucleotide Identity (ANI) data

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