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Full information on isolate VICE0394 (id:25330)

Provenance/primary metadata

id
25330
isolate
VICE0394
country
Iceland
continent
Europe
region
Reykjavík
year
2010
serotype
6A
age yr
2
diagnosis
otitis media
host
human
source
middle ear fluid
ENA accession
ERR470174 www.ebi.ac.uk
rMLST database accession
113723
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
2020-05-04

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
42
total length
2,129,735 bp
max length
228,841 bp
mean length
50,708 bp
N50 contig number
8
N50 length (L50)
101,159
N90 contig number
22
N90 length (L90)
38,696
N95 contig number
25
N95 length (L95)
24,325
loci tagged
1,403
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: 108 (39 isolates)
Sp_cgc_10cgMLSTSingle-linkage10experimentalgroup: 124 (3 isolates)
Sp_cgc_5cgMLSTSingle-linkage5experimentalgroup: 127 (3 isolates)

Schemes and loci

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Tools

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