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SJD2

Organism name:
Porphyromonas gingivalis SJD2 (CFB group bacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: SJD2
BioSample:
SAMN02470968
BioProject:
PRJNA205615
Submitter:
Shanghai Jiao Tong University School of Medicine
Date:
2013/12/04
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_000503975.1 (latest)
RefSeq assembly accession:
GCF_000503975.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
ASYL01
Assembly method:
SOAPdenovo v. 1.3
Expected final version:
yes
Genome coverage:
122.0x
Sequencing technology:
Illumina GAIIx

IDs: 84401 [UID] 867798 [GenBank] 873128 [RefSeq]

See Genome Information for Porphyromonas gingivalis

There are 112 assemblies for this organism

See more

History (Show revision history)

Comment

Annotation was modified by the submitter based on annotation generated by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
Bacteria and sourece DNA available from Dali Liu, Department of Periodontology, Shanghai ... Jiao Tong University School of Medicine, Ninth People's Hospital, Shanghai 200011, China  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::05/31/2013 17:58:52
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Software revision::2.0 (rev. 401101)
Features Annotated::Gene; CDS; rRNA; tRNA; repeat_region
Genes::2,135
CDS::2,020
Pseudo Genes::64
CRISPR Arrays::3
rRNAs::3 ( 5S, 16S, 23S )
tRNAs::48
Frameshifted Genes::12
##Genome-Annotation-Data-END##

Global statistics

Total sequence length2,329,548
Total ungapped length2,328,850
Gaps between scaffolds0
Number of scaffolds117
Scaffold N5037,197
Scaffold L5021
Number of contigs140
Contig N5032,167
Contig L5023
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)140

Supplemental Content

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
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
unplaced2,329,5481172,328,85037,197230

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Porphyromonas gingivalis SJD2Porphyromonas gingivalis

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_000010505.1Porphyromonas gingivalis ATCC 33277type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000010505.1Porphyromonas gingivalistype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type98.4386.0485.09
Best-match type98.4386.0485.09

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna