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ASM38377v1

Organism name:
Saccharomonospora halophila 8 (high G+C Gram-positive bacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: 8
BioSample:
SAMN02256397
BioProject:
PRJNA72359
Submitter:
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_000383775.1 (latest)
RefSeq assembly accession:
GCF_000383775.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
AICX01
Assembly method:
Newbler v. 2.3
Genome coverage:
Unknown
Sequencing technology:
454-GS-FLX-Titanium; Illumina GAii

IDs: 657178 [UID] 610358 [GenBank] 657178 [RefSeq]

See Genome Information for Saccharomonospora halophila

History (Show revision history)

Comment

URL -- http://www.jgi.doe.gov
JGI Project ID: 403390
Source DNA and Organism available from Hans-Peter Klenk (hpk@dsmz.de)
Source DNA available from Hans-Peter Klenk (hpk@dsmz.de)
Organism available from Hans-Peter Klenk (hpk@dsmz.de)
Contacts: Hans-Peter Klenk (hpk@dsmz.de)
 Tanja Woyke (microbe@cuba.jgi-psf.org)
Whole genome sequencing and draft assembly at JGI-PGF
Annotation by ... 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::Saccharomonospora halophila 8
collection_date::2002
lat_lon::28.90 48.18
depth::Missing
alt_elev::Missing
country::Kuwait
num_replicons::Missing
ref_biomaterial::DSM 44411, JCM 11761, CIP 107429
biotic_relationship::Free living
rel_to_oxygen::Aerobe
isol_growth_condt::11931168
assembly::Newbler v. 2.3
finishing_strategy::Missing
environment::Soil
trophic_level::Missing
sequencing_meth::WGS
GOLD Stamp ID::Gi07585
Current Finishing Status::Level 3: Improved-High-Quality Draft
Type Strain::Yes
Funding Program::DOE-CSP 2010
Gene Calling Method::Prodigal 1.4, GenePRIMP
Isolation Site::high salinity marsh soil
Isolation Comments::isolated by Al-Zarban SS et al
Motility::Nonmotile
Temperature Range::Mesophile
Temperature Optimum::28C
Salinity::Halophile
Gram Staining::Gram+
##MIGS-Data-END##

Global statistics

Total sequence length3,685,023
Total ungapped length3,632,223
Gaps between scaffolds0
Number of scaffolds116
Scaffold N5069,647
Scaffold L5016
Number of contigs644
Contig N506,831
Contig L50154
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)644

Supplemental Content

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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
unplaced3,685,0231163,632,22369,6475280

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Saccharomonospora halophila 8Saccharomonospora halophila

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
samena

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000430445.1Saccharomonospora iraqiensistype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type94.4477.5073.37

ANI result

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