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Full information on isolate VICE0402 (id:25306)

Provenance/primary metadata

id
25306
isolate
VICE0402
country
Iceland
continent
Europe
region
Kópavogi
year
2010
serotype
6A
age yr
1
diagnosis
otitis media
host
human
source
middle ear fluid
ENA accession
ERR470182 www.ebi.ac.uk
rMLST database accession
85524
sender
Angela Brueggemann, University of Oxford, UK
curator
Melissa Jansen van Rensburg, University of Oxford, UK (E-mail: Melissa.JansenvanRensburg@ndph.ox.ac.uk)
update history
11 updates show details
date entered
2015-03-17
datestamp
2020-04-03

Publications (2)

  • Quirk SJ, Haraldsson G, Erlendsdóttir H, Hjálmarsdóttir MÁ, van Tonder AJ, Hrafnkelsson B, Sigurdsson S, Bentley SD, Haraldsson Á, Brueggemann AB, Kristinsson KG (2018). Effect of Vaccination on Pneumococci Isolated from the Nasopharynx of Healthy Children and the Middle Ear of Children with Otitis Media in Iceland. J Clin Microbiol 56:
  • Rezaei Javan R, van Tonder AJ, King JP, Harrold CL, Brueggemann AB (2018). Genome Sequencing Reveals a Large and Diverse Repertoire of Antimicrobial Peptides. Front Microbiol 9:2012

Sequence bin

contigs
204
total length
2,134,627 bp
max length
98,150 bp
mean length
10,464 bp
N50 contig number
18
N50 length (L50)
37,381
N90 contig number
60
N90 length (L90)
9,986
N95 contig number
75
N95 length (L95)
5,367
loci tagged
1,405
detailed breakdown
Display

Similar isolates (determined by classification schemes)

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Sp_cgc_1000cgMLSTSingle-linkage1000experimentalgroup: 4 (827 isolates)
Sp_cgc_500cgMLSTSingle-linkage500experimentalgroup: 31 (114 isolates)
Sp_cgc_400cgMLSTSingle-linkage400experimentalgroup: 31 (114 isolates)
Sp_cgc_300cgMLSTSingle-linkage300experimentalgroup: 32 (114 isolates)
Sp_cgc_200cgMLSTSingle-linkage200experimentalgroup: 100 (113 isolates)
Sp_cgc_100cgMLSTSingle-linkage100experimentalgroup: 105 (64 isolates)
Sp_cgc_50cgMLSTSingle-linkage50experimentalgroup: 106 (63 isolates)
Sp_cgc_25cgMLSTSingle-linkage25experimentalgroup: 117 (11 isolates)
Sp_cgc_10cgMLSTSingle-linkage10experimentalgroup: 126 (4 isolates)
Sp_cgc_5cgMLSTSingle-linkage5experimentalgroup: 129 (4 isolates)

Schemes and loci

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Tools

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