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ASM1331827v2

Organism name:
Agrobacterium tumefaciens (Agrobacterium genomosp. 1)
Taxonomy check:
Inconclusive
Infraspecific name:
Strain: A74a
BioSample:
SAMN14165556
BioProject:
PRJNA607555
Submitter:
Oregon State University
Date:
2023/02/02
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
GenBank assembly accession:
GCA_013318275.2 (latest)
RefSeq assembly accession:
GCF_013318275.2 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Unicycler v. v0.4.9b
Expected final version:
yes
Genome coverage:
352.5x
Sequencing technology:
Illumina HiSeq; Oxford Nanopore MinION

IDs: 15767921 [UID] 40483848 [GenBank] 40546298 [RefSeq]

See Genome Information for Agrobacterium tumefaciens

Pathogen Detection Resources

There are 260 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/
Bacteria and source DNA available from Jeffrey H Chang

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Date::03/01/2024 04:05:15
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.6
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA
Genes (total)::5,180
CDSs (total)::5,109
Genes (coding)::5,043
CDSs (with protein)::5,043
Genes (RNA)::71
rRNAs::4, 4, 4 (5S, 16S, 23S)
complete rRNAs::4, 4, 4 (5S, 16S, 23S)
tRNAs::55
ncRNAs::4
Pseudo Genes (total)::66
CDSs (without protein)::66
Pseudo Genes (ambiguous residues)::0 of 66
Pseudo Genes (frameshifted)::27 of 66
Pseudo Genes (incomplete)::44 of 66
Pseudo Genes (internal stop)::11 of 66
Pseudo Genes (multiple problems)::14 of 66
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,477,231
Total ungapped length5,477,231
Total number of chromosomes and plasmids4

Supplemental Content

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Assembly Information

Related Information

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
Assembly Unit: Primary Assembly (GCF_013318295.2)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CircularCP116692.1=NZ_CP116692.1
Chromosome LinearCP116693.1=NZ_CP116693.1
Plasmid pAtA74a_aCP116694.1=NZ_CP116694.1
Plasmid pAtA74a_bCP116695.1=NZ_CP116695.1

Assembly statistics

MoleculeTotal
Length
All5,477,231
Chromosome Circular2,972,793
Chromosome Linear2,230,757
Plasmid pAtA74a_a145,563
Plasmid pAtA74a_b128,118

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Agrobacterium tumefaciensAgrobacterium tumefaciens

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_011684035.1Agrobacterium tumefacienssuspected-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000092025.1Agrobacterium fabrumtype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type87.1574.9269.45
Best-match type95.4583.1580.26

ANI result

Taxonomy check statusBest match statusComment
Inconclusivebelow-threshold-mismatchna