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ASM41452v1

Organism name:
Gardnerella vaginalis JCP8108 (high G+C Gram-positive bacteria)
Taxonomy check:
Inconclusive
Infraspecific name:
Strain: JCP8108
BioSample:
SAMN02436830
BioProject:
PRJNA181321
Submitter:
Washington University
Date:
2013/06/26
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_000414525.1 (latest)
RefSeq assembly accession:
GCF_000414525.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
ATJJ01
Assembly method:
Velvet v. 1.1.06
Genome coverage:
152x
Sequencing technology:
Illumina

IDs: 714368 [UID] 714368 [GenBank] 1357868 [RefSeq]

See Genome Information for Gardnerella vaginalis

There are 213 assemblies for this organism

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History (Show revision history)

Comment

Bacteria and source DNA were provided by Amanda Lewis, Ph.D. (Washington University School of Medicine, Department of Molecular Microbiology, Campus Box 8230 660 S. Euclid Ave. St. Louis, MO 63110).

Coding sequences were predicted using GeneMark and Glimmer3. Intergenic regions ... not spanned by GeneMark and Glimmer3 were blasted against NCBI's non-redundant (NR) database and predictions generated based on protein alignments. tRNA genes were determined using tRNAscan-SE and non-coding RNA genes by RNAmmer and Rfam. The final gene set is processed through several programs such as Kegg, psortB and Interproscan to determine possible function. Gene product names are determined by BER. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs.

This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC.

This work was funded in part by the March of Dimes Basil O'Connor award and the National Human Genome Research Institute (NHGRI)/National Institutes of Health (NIH) for characterization of this genome.  more

Global statistics

Total sequence length1,665,594
Total ungapped length1,663,094
Gaps between scaffolds0
Number of scaffolds151
Scaffold N5031,929
Scaffold L5018
Number of contigs176
Contig N5030,383
Contig L5019
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)176

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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
unplaced1,665,5941511,663,09431,929250

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Gardnerella vaginalis JCP8108Gardnerella vaginalis

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_001042655.1Gardnerella vaginalis ATCC 14018 = JCM 11026type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_001042655.1Gardnerella vaginalistype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type95.3485.9485.72
Best-match type95.3485.9485.72

ANI result

Taxonomy check statusBest match statusComment
Inconclusivebelow-threshold-matchna