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ASM1331855v1

Organism name:
Agrobacterium tumefaciens (Agrobacterium genomosp. 1)
Taxonomy check:
Inconclusive
Infraspecific name:
Strain: 17-713-1if
BioSample:
SAMN14165599
BioProject:
PRJNA607555
Submitter:
Oregon State University
Date:
2020/06/10
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_013318555.1 (latest)
RefSeq assembly accession:
GCF_013318555.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
JAAMAA01
Assembly method:
SPAdes v. 3.13.1
Expected final version:
yes
Genome coverage:
85x
Sequencing technology:
Illumina HiSeq

IDs: 7258321 [UID] 19999408 [GenBank] 20056738 [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 15:03:42
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)::5,391
CDSs (total)::5,334
Genes (coding)::5,206
CDSs (with protein)::5,206
Genes (RNA)::57
rRNAs::1, 1, 1 (5S, 16S, 23S)
complete rRNAs::1, 1, 1 (5S, 16S, 23S)
tRNAs::50
ncRNAs::4
Pseudo Genes (total)::128
CDSs (without protein)::128
Pseudo Genes (ambiguous residues)::0 of 128
Pseudo Genes (frameshifted)::52 of 128
Pseudo Genes (incomplete)::92 of 128
Pseudo Genes (internal stop)::15 of 128
Pseudo Genes (multiple problems)::25 of 128
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,636,829
Total ungapped length5,636,010
Gaps between scaffolds0
Number of scaffolds95
Scaffold N50123,291
Scaffold L5014
Number of contigs98
Contig N50123,291
Contig L5015
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)95

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
unplaced5,636,829955,636,010123,29130

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_015704895.1Agrobacterium leguminumtype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type87.6071.5868.29
Best-match type96.0178.7781.15

ANI result

Taxonomy check statusBest match statusComment
Inconclusivemismatchcoverage is less than 80%