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ASM1612737v1

  • Anomalous assembly.
Organism name:
Lactococcus garvieae (firmicutes)
Taxonomy check:
Failed
Infraspecific name:
Strain: FDAARGOS_1002
BioSample:
SAMN16357171
BioProject:
PRJNA231221
Submitter:
US Food and Drug Administration
Date:
2020/12/20
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
Assembly anomaly:
unverified source organism
Excluded from RefSeq:
  • unverified source organism
GenBank assembly accession:
GCA_016127375.1 (latest)
RefSeq assembly accession:
GCF_016127375.1 (suppressed)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
SMRT v. 7.1.0, HGAP v. 4, SPAdes v. 3.11.1
Genome coverage:
2849.44x
Sequencing technology:
Pacbio; Illumina

IDs: 8871361 [UID] 24000908 [GenBank] 24050228 [RefSeq]

See Genome Information for Lactococcus garvieae

Pathogen Detection Resources

There are 109 assemblies for this organism

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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::12/09/2020 15:16:57
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::5.0
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::2,331
CDSs (total)::2,249
Genes (coding)::2,130
CDSs (with protein)::2,130
Genes (RNA)::82
rRNAs::6, 5, 5 (5S, 16S, 23S)
complete rRNAs::6, 5, 5 (5S, 16S, 23S)
tRNAs::63
ncRNAs::3
Pseudo Genes (total)::119
CDSs (without protein)::119
Pseudo Genes (ambiguous residues)::0 of 119
Pseudo Genes (frameshifted)::59 of 119
Pseudo Genes (incomplete)::54 of 119
Pseudo Genes (internal stop)::20 of 119
Pseudo Genes (multiple problems)::14 of 119
##Genome-Annotation-Data-END##

Global statistics

Total sequence length2,292,159
Total ungapped length2,292,159
Total number of chromosomes and plasmids6

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Assembly Information

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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
Assembly Unit: Primary Assembly (GCA_016127385.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP066003.1=NZ_CP066003.1
Plasmid unnamed1CP066000.1=NZ_CP066000.1
Plasmid unnamed2CP066001.1=NZ_CP066001.1
Plasmid unnamed3CP066002.1=NZ_CP066002.1
Plasmid unnamed4CP066004.1=NZ_CP066004.1
Plasmid unnamed5CP066005.1=NZ_CP066005.1

Assembly statistics

MoleculeTotal
Length
All2,292,159
Chromosome 2,144,048
Plasmid unnamed121,208
Plasmid unnamed246,056
Plasmid unnamed342,274
Plasmid unnamed420,747
Plasmid unnamed517,826

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Lactococcus garvieaeLactococcus garvieae

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_016026695.1Lactococcus garvieaetype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_002154895.1Lactococcus petauritype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type93.9473.0980.38
Best-match type98.0979.0975.62

ANI result

Taxonomy check statusBest match statusComment
Failedmismatchna