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ASM1332083v1

Organism name:
Agrobacterium rubi (a-proteobacteria)
Taxonomy check:
Inconclusive
Infraspecific name:
Strain: Eu3-2NK
BioSample:
SAMN14165485
BioProject:
PRJNA607555
Submitter:
Oregon State University
Date:
2020/06/10
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_013320835.1 (latest)
RefSeq assembly accession:
GCF_013320835.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
JAANSA01
Assembly method:
SPAdes v. 3.13.1
Expected final version:
yes
Genome coverage:
44x
Sequencing technology:
Illumina HiSeq

IDs: 7259461 [UID] 20001688 [GenBank] 20054918 [RefSeq]

See Genome Information for Agrobacterium rubi

There are 11 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::03/09/2020 23:42:57
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)::5,302
CDSs (total)::5,244
Genes (coding)::5,119
CDSs (with protein)::5,119
Genes (RNA)::58
rRNAs::4, 1, 1 (5S, 16S, 23S)
complete rRNAs::4, 1, 1 (5S, 16S, 23S)
tRNAs::48
ncRNAs::4
Pseudo Genes (total)::125
CDSs (without protein)::125
Pseudo Genes (ambiguous residues)::0 of 125
Pseudo Genes (frameshifted)::60 of 125
Pseudo Genes (incomplete)::74 of 125
Pseudo Genes (internal stop)::19 of 125
Pseudo Genes (multiple problems)::25 of 125
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,572,671
Total ungapped length5,571,766
Gaps between scaffolds0
Number of scaffolds37
Scaffold N50314,623
Scaffold L507
Number of contigs38
Contig N50314,623
Contig L507
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)37

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
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced5,572,671375,571,766314,62310

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Agrobacterium rubiAgrobacterium rubi

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_017873055.1Agrobacterium rubisuspected-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_017873055.1Agrobacterium rubisuspected-type

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type95.9181.2785.58
Best-match type95.9181.2785.58

ANI result

Taxonomy check statusBest match statusComment
Inconclusivebelow-threshold-matchna