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ASM31751v1

Organism name:
Allocoleopsis franciscana PCC 7113 (cyanobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: PCC 7113
BioSample:
SAMN02261351
BioProject:
PRJNA158839
Submitter:
JGI
Date:
2012/12/06
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_000317515.1 (latest)
RefSeq assembly accession:
GCF_000317515.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Newbler v. 2.3 (pre-release), VELVET v. 1.0.13, Parallel phrap v. 4.24 SPS
Genome coverage:
30x
Sequencing technology:
454/Illumina

IDs: 504098 [UID] 503898 [GenBank] 504098 [RefSeq]

See Genome Information for Allocoleopsis franciscana

Pathogen Detection Resources

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: 4089897
Source DNA and Organism available from Cheryl A. Kerfeld (CKerfeld@lbl.gov)
 Contacts: Cheryl A. Kerfeld (CKerfeld@lbl.gov)
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)  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Date::10/08/2023 15:15:03
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.6
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA
Genes (total)::6,782
CDSs (total)::6,695
Genes (coding)::6,525
CDSs (with protein)::6,525
Genes (RNA)::87
rRNAs::4, 4, 4 (5S, 16S, 23S)
complete rRNAs::4, 4, 4 (5S, 16S, 23S)
tRNAs::71
ncRNAs::4
Pseudo Genes (total)::170
CDSs (without protein)::170
Pseudo Genes (ambiguous residues)::0 of 170
Pseudo Genes (frameshifted)::53 of 170
Pseudo Genes (incomplete)::128 of 170
Pseudo Genes (internal stop)::12 of 170
Pseudo Genes (multiple problems)::21 of 170
CRISPR Arrays::11
##Genome-Annotation-Data-END##

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Microcoleus sp. PCC 7113
collection_date::1971
lat_lon::37.774 122.419
depth::Missing
alt_elev::Missing
country::USA
environment::Soil
num_replicons::9
ref_biomaterial::PCC 7113, ATCC 29206
biotic_relationship::Free living
trophic_level::Chemoheterotroph
rel_to_oxygen::Anaerobe
isol_growth_condt::Missing
sequencing_meth::WGS
assembly::Newbler v. 2.3 (pre-release), VELVET v. 1.0.13, Parallel phrap v. 4.24 SPS
finishing_strategy::Finished
GOLD Stamp ID::Gi05876
Type Strain::No
Funding Program::DOE-GEBA 2009
Gene Calling Method::GenePrimp, Prodigal 1.4
Isolation Site::Soil, orchid house, San Francisco, USA, 1971
Motility::Motile
Temperature Range::Mesophile
Diseases::None
##MIGS-Data-END##

Global statistics

Total sequence length7,966,510
Total ungapped length7,966,510
Total number of chromosomes and plasmids9

Supplemental Content

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Assembly Information

Related Information

PubMed articles for this assembly

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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_000317525.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP003630.1=NC_019738.1
Plasmid pMIC7113.01CP003631.1=NC_019739.1
Plasmid pMIC7113.02CP003632.1=NC_019760.1
Plasmid pMIC7113.03CP003633.1=NC_019740.1
Plasmid pMIC7113.04CP003634.1=NC_019761.1
Plasmid pMIC7113.05CP003635.1=NC_019741.1
Plasmid pMIC7113.06CP003636.1=NC_019742.1
Plasmid pMIC7113.07CP003637.1=NC_019762.1
Plasmid pMIC7113.08CP003638.1=NC_019743.1

Assembly statistics

MoleculeTotal
Length
All7,966,510
Chromosome 7,470,429
Plasmid pMIC7113.01146,045
Plasmid pMIC7113.0293,032
Plasmid pMIC7113.0392,471
Plasmid pMIC7113.0450,464
Plasmid pMIC7113.0538,468
Plasmid pMIC7113.0628,816
Plasmid pMIC7113.0725,982
Plasmid pMIC7113.0820,803

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Allocoleopsis franciscana PCC 7113Allocoleopsis franciscana

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
samena

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_003990575.1Chlorogloeopsis fritschiitype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type84.900.210.22

ANI result

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