PROJECT INFORMATION
GOLD Project ID
Gp0012802  
Project Name
Capnocytophaga ochracea Holt 25  
Other Names
  
Legacy ER Project ID
6179  
Legacy GOLD ID
Gi10958  
NCBI BioProject Name Capnocytophaga ochracea str. Holt 25
NCBI BioProject ID 78899
NCBI BioProject Accession PRJNA78899
NCBI Locus Tag
HMPREF1319  
NCBI BioSample Accession SAMN00792203
PI Dodson R.
Added By Ionna Pagani on 2011-11-29
Last Modified By JGI automated process on 2014-03-26
Project Comments
  
Project Status
Permanent Draft  
Project Relevance Human Microbiome Project (HMP)
Medical
Sequencing Center J. Craig Venter Institute (JCVI) (USA)
Collaborating Institute
  
Funding Agency NIH (USA)
Project Description
HMP reference genome  
Is JGI Project
  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
Project Information
  
Database
  
Genome Publications
  
Other Publications
  
SRA Experiment
 
SRA Experiment Id SRX121839
Experiment Title 1132455235502 HMP292 Capnocytophaga ochracea ATCC 33596 HMP292-PE-ILI79-1 Experiment
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name HMP292-PE-ILI79-1
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
Spot Length 200
PROJECT COMPOSITION
Study Human Microbiome Project (HMP) Reference Genomes
Organism Capnocytophaga ochracea Holt 25
Analysis Projects Capnocytophaga ochracea Holt 25
Number of Analysis Projects 1
Number of DAPs
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31) Level 2: High-Quality Draft
Finishing Goal Level 2: High-Quality Draft
Sequencing Comments
  
Sequencing Technology (MIGS-29) Illumina HiSeq 2000
Library Method (MIGS-28)
  
Number Of Reads
856240  
Read Size
  
Vector
  
GC Percent
40  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0012802
Organism Name
Capnocytophaga ochracea Holt 25  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
BACTEROIDETES  
Genus
Capnocytophaga  
Genus Synonyms
  
Species
Capnocytophaga ochracea  
Subspecies
  
Species Synonyms
  
Strain
Holt 25  
Strain Synonyms
  
Serovar/Cultivar
ATCC 33596 , CCUG 15407 , DSM 7272 , KCTC 3693 , LMG 11546   
Culture Collection ID
ATCC 33596  
Type Strain
Yes  
Exemplar DOI
10.1601/ex.7969  
Exemplar Name
Capnocytophaga ochracea  
Taxon DOI
10.1601/tx.8134  
Biosafety Level
2  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 1125719
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Bacteroidetes  
NCBI Class
Flavobacteriia  
NCBI Order
Flavobacteriales  
NCBI Family
Flavobacteriaceae  
NCBI Genus
Capnocytophaga  
NCBI Species
Capnocytophaga ochracea  
ISOLATION CLASSIFICATION
Ecosystem
Host-associated  
Ecosystem Category
Human  
Ecosystem Type
Digestive system  
Ecosystem Subtype
Oral  
Specific Ecosystem
Unclassified  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
  
Cell Shape
  
Motility
  
Sporulation
  
Temperature Range
Mesophile  
Temperature Optimum
37  
Salinity
  
pH
  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
Gram-  
Biotic Relationships
  
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats Host
Human oral cavity
Metabolisms
  
Phenotypes
  
Energy Sources
  
HMP METADATA
HMP ID
1319  
Show in DACC?
Yes  
HMP Project Status
Complete  
BEI Status
  
NCBI Submission Status
6. annotation (and sequence) public on NCBI site  
Isolate Suggestion Source
  
HMP Isolation Body Sample Site
Oral  
HMP Isolation Body Sample Subsite
  
HMP Finishing Goal
  
Source, Sample & Medical Relevance Comments
  
Isolate Availability Comments
  
Project Comments
  
DNA Received
Yes  
Date DNA Received
2011-07-14  
Date Sequencing Begins
2011-09-07  
Date Draft Sequencing Completed
2011-10-03  
Cross Reference ID
  

 

 

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