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Full information on isolate VICE0420 (id:25291)

Provenance/primary metadata

id
25291
isolate
VICE0420
country
Iceland
continent
Europe
region
Reykjavík
year
2010
serotype
6A
age yr
1
diagnosis
otitis media
host
human
source
middle ear fluid
ENA accession
ERR470200 www.ebi.ac.uk
rMLST database accession
84495
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
2020-03-04

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
203
total length
2,098,800 bp
max length
90,880 bp
mean length
10,339 bp
N50 contig number
20
N50 length (L50)
37,100
N90 contig number
62
N90 length (L90)
8,169
N95 contig number
79
N95 length (L95)
4,721
loci tagged
1,408
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: 94 (7 isolates)
Sp_cgc_400cgMLSTSingle-linkage400experimentalgroup: 95 (7 isolates)
Sp_cgc_300cgMLSTSingle-linkage300experimentalgroup: 97 (5 isolates)
Sp_cgc_200cgMLSTSingle-linkage200experimentalgroup: 102 (5 isolates)
Sp_cgc_100cgMLSTSingle-linkage100experimentalgroup: 107 (5 isolates)
Sp_cgc_50cgMLSTSingle-linkage50experimentalgroup: 108 (5 isolates)
Sp_cgc_25cgMLSTSingle-linkage25experimentalgroup: 111 (5 isolates)
Sp_cgc_10cgMLSTSingle-linkage10experimentalgroup: 116 (5 isolates)
Sp_cgc_5cgMLSTSingle-linkage5experimentalgroup: 116 (4 isolates)

Schemes and loci

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Tools

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