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ASM228354v1

  • Anomalous assembly.
Organism name:
Salmonella enterica subsp. enterica serovar Typhimurium (enterobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: GMR-S-1454
BioSample:
SAMN05792026
BioProject:
PRJNA343664
Submitter:
International Center for Microbial Genomics - Universidad El Bosque
Date:
2017/08/31
Assembly type:
na
Assembly level:
Contig
Genome representation:
full
Assembly anomaly:
contaminated
Excluded from RefSeq:
  • contaminated
GenBank assembly accession:
GCA_002283545.1 (latest)
RefSeq assembly accession:
GCF_002283545.1 (suppressed)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
MVPQ01
Assembly method:
CLC Genomics Workbench v. 8.5
Expected final version:
yes
Genome coverage:
65x
Sequencing technology:
Illumina MiSeq

IDs: 1188201 [UID] 4984508 [GenBank] 4988148 [RefSeq]

See Genome Information for Salmonella enterica

There are 525275 assemblies for this organism

See more

History (Show revision history)

Comment

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/

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::04/12/2017 14:00:03
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Software revision::4.1
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::5,397
CDS (total)::5,291
Genes (coding)::5,144
CDS (coding)::5,144
Genes (RNA)::106
rRNAs::4, 2, 8 (5S, 16S, 23S)
complete rRNAs::4 (5S)
partial rRNAs::2, 8 (16S, 23S)
tRNAs::77
ncRNAs::15
Pseudo Genes (total)::147
Pseudo Genes (ambiguous residues)::0 of 147
Pseudo Genes (frameshifted)::71 of 147
Pseudo Genes (incomplete)::59 of 147
Pseudo Genes (internal stop)::59 of 147
Pseudo Genes (multiple problems)::36 of 147
CRISPR Arrays::3
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,157,016
Total ungapped length5,157,016
Number of contigs213
Contig N5050,425
Contig L5031
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)213

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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
unplaced5,157,0162135,157,01650,42500

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 type99.9690.5694.32
Best-match type99.9690.5694.32

ANI result

Taxonomy check statusBest match statusComment
OKderived-species-matchna