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ASM34683v2

Organism name:
Helicobacter pylori GAMchJs117Ai (e-proteobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: GAMchJs117Ai
BioSample:
SAMN02436921
BioProject:
PRJNA89293
Submitter:
Washington University
Date:
2013/03/21
Assembly type:
na
Release type:
minor
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_000346835.2 (latest)
RefSeq assembly accession:
GCF_000346835.2 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
APEK01
Assembly method:
Velvet v. 1.1.04
Genome coverage:
91x
Sequencing technology:
Illumina

IDs: 550561 [UID] 2492608 [GenBank] 2497958 [RefSeq]

See Genome Information for Helicobacter pylori

There are 4493 assemblies for this organism

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History (Show revision history)

Comment

Helicobacter pylori GAMchJs117Ai is a member of the Proteobacteria division of the domain Bacteria and has been isolated from the gastrointestinal tract.

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

Bacteria and source DNA were provided by Martin Antonio, PhD & Ousman Secka (Medical Research Council (MRC) Unit, The Gambia, PO Box 273, Banjul, The Gambia). The project was funded by Medical Research Council (UK)

Coding sequences were predicted using GeneMark v3.3 and Glimmer3 v3.02. 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 1.23 and non-coding RNA genes by RNAmmer-1.2 and Rfam v8.1. The final gene set is processed through several programs such as Kegg (Release 56), psortB (Version 3.0.3) and Interproscan (Version 4.7) to determine possible function. Gene product names are determined by BER (Version 2.5). Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs. 

The National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH) is funding the sequence characterization of the Helicobacter pylori GAMchJs117Ai genome.  more

Global statistics

Total sequence length1,612,146
Total ungapped length1,611,686
Gaps between scaffolds0
Number of scaffolds49
Scaffold N5078,209
Scaffold L507
Number of contigs72
Contig N5055,909
Contig L5010
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)72

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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
unplaced1,612,146491,611,68678,209230

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Helicobacter pylori GAMchJs117AiHelicobacter pylori

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_001312765.1Helicobacter pyloritype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_001312765.1Helicobacter pyloritype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type93.7789.5590.13
Best-match type93.7789.5590.13

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna