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Full information on isolate VICE0287 (id:25303)

Provenance/primary metadata

id
25303
isolate
VICE0287
country
Iceland
continent
Europe
region
Reykjavík
year
2009
serotype
6A
age yr
1
diagnosis
otitis media
host
human
source
middle ear fluid
ENA accession
ERR449729 www.ebi.ac.uk
rMLST database accession
95359
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
15 updates show details
date entered
2015-03-17
datestamp
2020-04-23

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
196
total length
2,133,869 bp
max length
94,887 bp
mean length
10,888 bp
N50 contig number
17
N50 length (L50)
40,969
N90 contig number
58
N90 length (L90)
9,539
N95 contig number
72
N95 length (L95)
5,269
loci tagged
1,404
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: 104 (47 isolates)
Sp_cgc_50cgMLSTSingle-linkage50experimentalgroup: 105 (36 isolates)
Sp_cgc_25cgMLSTSingle-linkage25experimentalgroup: 106 (22 isolates)

Schemes and loci

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