U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Download Assembly



ASM1331883v1

Organism name:
Agrobacterium tumefaciens (Agrobacterium genomosp. 1)
Taxonomy check:
Inconclusive
Infraspecific name:
Strain: 17-712-1iv_(b)
BioSample:
SAMN14165607
BioProject:
PRJNA607555
Submitter:
Oregon State University
Date:
2020/06/10
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_013318835.1 (latest)
RefSeq assembly accession:
GCF_013318835.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
JAAMAR01
Assembly method:
SPAdes v. 3.13.1
Expected final version:
yes
Genome coverage:
54x
Sequencing technology:
Illumina HiSeq

IDs: 7258471 [UID] 19999708 [GenBank] 20056638 [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 15:36:51
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)::5,366
CDSs (total)::5,310
Genes (coding)::5,185
CDSs (with protein)::5,185
Genes (RNA)::56
rRNAs::1, 1, 1 (5S, 16S, 23S)
complete rRNAs::1, 1, 1 (5S, 16S, 23S)
tRNAs::49
ncRNAs::4
Pseudo Genes (total)::125
CDSs (without protein)::125
Pseudo Genes (ambiguous residues)::0 of 125
Pseudo Genes (frameshifted)::51 of 125
Pseudo Genes (incomplete)::92 of 125
Pseudo Genes (internal stop)::15 of 125
Pseudo Genes (multiple problems)::27 of 125
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,637,943
Total ungapped length5,637,212
Gaps between scaffolds0
Number of scaffolds73
Scaffold N50271,006
Scaffold L507
Number of contigs75
Contig N50256,242
Contig L508
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)73

Supplemental Content

PubMed articles for this assembly

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

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
unplaced5,637,943735,637,212271,00620

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 type87.6071.6668.38
Best-match type96.0178.7781.16

ANI result

Taxonomy check statusBest match statusComment
Inconclusivemismatchcoverage is less than 80%