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ASM1331789v1

Organism name:
Agrobacterium tumefaciens (Agrobacterium genomosp. 1)
Taxonomy check:
OK
Infraspecific name:
Strain: J3/75
BioSample:
SAMN14165476
BioProject:
PRJNA607555
Submitter:
Oregon State University
Date:
2020/06/10
Assembly type:
na
Assembly level:
Contig
Genome representation:
full
GenBank assembly accession:
GCA_013317895.1 (latest)
RefSeq assembly accession:
GCF_013317895.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
JAALYY01
Assembly method:
SPAdes v. 3.13.1
Expected final version:
yes
Genome coverage:
84x
Sequencing technology:
Illumina HiSeq

IDs: 7257991 [UID] 19998748 [GenBank] 20055478 [RefSeq]

See Genome Information for Agrobacterium tumefaciens

There are 259 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::02/28/2020 17:55:42
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::4.11
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::5,282
CDSs (total)::5,226
Genes (coding)::5,122
CDSs (with protein)::5,122
Genes (RNA)::56
rRNAs::1, 1, 1 (5S, 16S, 23S)
complete rRNAs::1, 1 (5S, 16S)
partial rRNAs::1 (23S)
tRNAs::49
ncRNAs::4
Pseudo Genes (total)::104
CDSs (without protein)::104
Pseudo Genes (ambiguous residues)::0 of 104
Pseudo Genes (frameshifted)::45 of 104
Pseudo Genes (incomplete)::64 of 104
Pseudo Genes (internal stop)::18 of 104
Pseudo Genes (multiple problems)::20 of 104
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,626,859
Total ungapped length5,626,859
Number of contigs45
Contig N50586,401
Contig L503
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)45

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
unplaced5,626,859455,626,859586,40100

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_011684035.1Agrobacterium tumefacienssuspected-type

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type99.0388.1983.99
Best-match type99.0388.1983.99

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna