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ASM1105801v1

Organism name:
Salmonella enterica subsp. enterica serovar Typhimurium (enterobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: ISU-SAL244-16
BioSample:
SAMN12906840
BioProject:
PRJNA575700
Submitter:
Iowa State University College of Veterinary Medicine
Date:
2020/03/02
Assembly type:
na
Assembly level:
Contig
Genome representation:
full
GenBank assembly accession:
GCA_011058015.1 (latest)
RefSeq assembly accession:
GCF_011058015.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
WIDF01
Assembly method:
SPAdes v. 3.9.0
Expected final version:
yes
Genome coverage:
20x
Sequencing technology:
Illumina MiSeq

IDs: 6095161 [UID] 17339678 [GenBank] 17346738 [RefSeq]

See Genome Information for Salmonella enterica

There are 525610 assemblies for this organism

See more

History (Show revision history)

Comment

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/

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::10/28/2019 10:27:58
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::4.10
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::5,132
CDSs (total)::5,015
Genes (coding)::4,909
CDSs (with protein)::4,909
Genes (RNA)::117
rRNAs::7, 7, 7 (5S, 16S, 23S)
complete rRNAs::5 (5S)
partial rRNAs::2, 7, 7 (5S, 16S, 23S)
tRNAs::79
ncRNAs::17
Pseudo Genes (total)::106
CDSs (without protein)::106
Pseudo Genes (ambiguous residues)::0 of 106
Pseudo Genes (frameshifted)::40 of 106
Pseudo Genes (incomplete)::67 of 106
Pseudo Genes (internal stop)::24 of 106
Pseudo Genes (multiple problems)::23 of 106
CRISPR Arrays::3
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,087,592
Total ungapped length5,087,592
Number of contigs135
Contig N50162,461
Contig L5010
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)135

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Contig
Count
Ungapped
Length
Contig
N50
Spanned
Gaps
Unspanned
Gaps
unplaced5,087,5921355,087,592162,46100

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Salmonella enterica subsp. enterica serovar TyphimuriumSalmonella enterica

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_000006945.2Salmonella enterica subsp. enterica serovar Typhimurium str. LT2type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000006945.2Salmonella entericatype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type99.9692.8495.40
Best-match type99.9692.8495.40

ANI result

Taxonomy check statusBest match statusComment
OKderived-species-matchna