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ASM31779v1

Organism name:
Caldisphaera lagunensis DSM 15908 (crenarchaeotes)
Taxonomy check:
OK
Infraspecific name:
Culture-collection: DSM:15908
Infraspecific name:
Strain: DSM 15908
BioSample:
SAMN02261426
BioProject:
PRJNA70815
Submitter:
JGI
Date:
2012/12/10
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
RefSeq category:
representative genome
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000317795.1 (latest)
RefSeq assembly accession:
GCF_000317795.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Newbler v. 2.3
Genome coverage:
30x
Sequencing technology:
454/Illumina

IDs: 505098 [UID] 504598 [GenBank] 505098 [RefSeq]

See Genome Information for Caldisphaera lagunensis

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/
URL -- http://www.jgi.doe.gov
JGI Project ID: 4085239
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: Jonathan A. Eisen (jaeisen@ucdavis.edu)
 David Bruce (microbe@cuba.jgi-psf.org)
Whole genome sequencing and draft assembly at JGI-PGF
Finishing done by JGI-LANL
Annotation by JGI-ORNL and JGI-PGF
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)  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Name::GCF_000317795.1-RS_2024_05_02
Annotation Date::05/02/2024 01:00:39
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.7
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA
Genes (total)::1,570
CDSs (total)::1,519
Genes (coding)::1,515
CDSs (with protein)::1,515
Genes (RNA)::51
rRNAs::1, 1, 1 (5S, 16S, 23S)
complete rRNAs::1, 1, 1 (5S, 16S, 23S)
tRNAs::46
ncRNAs::2
Pseudo Genes (total)::4
CDSs (without protein)::4
Pseudo Genes (ambiguous residues)::0 of 4
Pseudo Genes (frameshifted)::1 of 4
Pseudo Genes (incomplete)::3 of 4
Pseudo Genes (internal stop)::1 of 4
Pseudo Genes (multiple problems)::1 of 4
##Genome-Annotation-Data-END##

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Caldisphaera lagunensis DSM 15908
collection_date::Missing
lat_lon::Missing
depth::Missing
alt_elev::Missing
country::Phillipines
environment::Fresh water, Hot spring
num_replicons::1
ref_biomaterial::DSM 15908, ANMR 0165, JCM 11604, MCC-UPLB 1331
biotic_relationship::Free living
trophic_level::Heterotroph
rel_to_oxygen::Anaerobe
isol_growth_condt::Missing
sequencing_meth::WGS
assembly::Newbler v. 2.3 (pre-release)
finishing_strategy::Finished
GOLD Stamp ID::Gi02911
Type Strain::Yes
Greengenes ID::78319
Funding Program::DOE-GEBA 2007
Gene Calling Method::Prodigal 1.4, GenePRIMP
Isolation Site::An acidic hot spring; Philippines
Cell Shape::Coccus-shaped
Temperature Range::Hyperthermophile
Temperature Optimum::75C
Gram Staining::Gram-
Phenotypes::Acidophile
##MIGS-Data-END##

Global statistics

Total sequence length1,546,846
Total ungapped length1,546,846
Total number of chromosomes and plasmids1

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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
Assembly Unit: Primary Assembly (GCF_000317805.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP003378.1=NC_019791.1

Assembly statistics

MoleculeTotal
Length
Chromosome 1,546,846

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Caldisphaera lagunensis DSM 15908Caldisphaera lagunensis

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
samena

Best-matching type-strain assembly

AssemblySpecies nameType category
none-foundnana

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match typena0.000.00

ANI result

Taxonomy check statusBest match statusComment
OKnaAssembly is the type-strain, no match is expected