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ASM38341v1

Organism name:
Hyphomicrobium zavarzinii ATCC 27496 (a-proteobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: ZV-622
BioSample:
SAMN02440966
BioProject:
PRJNA183046
Submitter:
DOE Joint Genome Institute
Date:
2013/04/26
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000383415.1 (latest)
RefSeq assembly accession:
GCF_000383415.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
ARTG01
Assembly method:
Velvet v. 1.1.04; ALLPATHS v. r42328
Genome coverage:
Unknown
Sequencing technology:
Illumina HiSeq 2000

IDs: 667058 [UID] 610808 [GenBank] 667058 [RefSeq]

See Genome Information for Hyphomicrobium zavarzinii

There are 4 assemblies for this organism

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History (Show revision history)

Comment

URL -- http://www.jgi.doe.gov
JGI Project ID: 1008099
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::Hyphomicrobium zavarzinii ATCC 27496
collection_date::Missing
lat_lon::Missing
depth::Missing
alt_elev::Missing
country::Missing
num_replicons::Missing
ref_biomaterial::ATCC 27496, DSM 1566, VKM B-2174
biotic_relationship::Missing
rel_to_oxygen::Missing
isol_growth_condt::Missing
assembly::Velvet v. 1.1.04; ALLPATHS v. r42328
finishing_strategy::Missing
environment::Soil
trophic_level::Missing
sequencing_meth::WGS
GOLD Stamp ID::Gi21319
Type Strain::Yes
Isolation Site::Soil, Moscow, USSR
Gram Staining::Gram-
##MIGS-Data-END##

Global statistics

Total sequence length4,651,795
Total ungapped length4,646,325
Gaps between scaffolds0
Number of scaffolds15
Scaffold N50666,181
Scaffold L503
Number of contigs20
Contig N50499,297
Contig L504
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)20

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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
unplaced4,651,795154,646,325666,18150

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Hyphomicrobium zavarzinii ATCC 27496Hyphomicrobium zavarzinii

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
samena

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000503895.1Hyphomicrobium nitrativoranstype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type82.4612.3615.72

ANI result

Taxonomy check statusBest match statusComment
OKbelow-threshold-mismatchAssembly is the type-strain, mismatch is within genus and expected