U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Download Assembly



ASM38236v1

Organism name:
Pannonibacter phragmitetus DSM 14782 (a-proteobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: DSM 14782
BioSample:
SAMN02441652
BioProject:
PRJNA187116
Submitter:
DOE Joint Genome Institute
Date:
2013/04/24
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000382365.1 (latest)
RefSeq assembly accession:
GCF_000382365.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
ARNQ01
Assembly method:
Velvet v. 1.1.04; ALLPATHS v. r41043
Genome coverage:
Unknown
Sequencing technology:
Illumina HiSeq 2000

IDs: 665658 [UID] 607628 [GenBank] 665658 [RefSeq]

See Genome Information for Pannonibacter phragmitetus

There are 7 assemblies for this organism

See more

History (Show revision history)

Comment

URL -- http://www.jgi.doe.gov
JGI Project ID: 406562
Source DNA and organism available from Hans-Peter Klenk at the German Collection of Microorganisms and Cell Cultures (DSMZ) (hans-peter.klenk@dsmz.de)
Contacts: Nikos Kyrpides (nckyrpides@lbl.gov)
 Tanja Woyke (microbe@cuba.jgi-psf.org)
Whole genome sequencing and draft assembly at JGI-PGF
Annotation by JGI-PGF ... and JGI-ORNL
The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. It is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis.
(http://www.genome.gov/page.cfm?pageID=10506376)
Full annotations are available from IMG  more

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Pannonibacter phragmitetus DSM 14782
collection_date::1998
lat_lon::47.7125 16.6995
depth::Missing
alt_elev::Missing
country::Hungary
num_replicons::Missing
ref_biomaterial::DSM 14782
biotic_relationship::Missing
rel_to_oxygen::Facultative
isol_growth_condt::12710626
assembly::Velvet v. 1.1.04; ALLPATHS v. r41043
finishing_strategy::Missing
environment::Soda lakes; Plants
trophic_level::Chemoorganotroph
sequencing_meth::WGS
GOLD Stamp ID::Gi11742
Type Strain::Yes
Funding Program::DOE-CSP 2012
Isolation Site::Surface of decomposing rhizomes of reed
Cell Shape::Rod-shaped
Motility::Motile
Sporulation::Nonsporulating
Temperature Range::Mesophile
Temperature Optimum::22-28 C
pH::7.0-11.0
Gram Staining::Gram-
Phenotypes::Alkalitolerant; Catalase positive
##MIGS-Data-END##

Global statistics

Total sequence length4,783,755
Total ungapped length4,780,110
Gaps between scaffolds0
Number of scaffolds40
Scaffold N50214,804
Scaffold L506
Number of contigs46
Contig N50214,804
Contig L506
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)46

Supplemental Content

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
unplaced4,783,755404,780,110214,80460

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Pannonibacter phragmitetus DSM 14782Pannonibacter phragmitetus

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_900454465.1Pannonibacter phragmitetussuspected-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_900454465.1Pannonibacter phragmitetussuspected-type

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type100.0099.9698.78
Best-match type100.0099.9698.78

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna
Support Center