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Full information on isolate VICE1177 (id:25334)

Provenance/primary metadata

id
25334
isolate
VICE1177
country
Iceland
continent
Europe
region
Hafnarfjörður
year
2011
serotype
6A
age yr
2
diagnosis
carriage
host
human
source
nasopharynx
ENA accession
ERR540673 www.ebi.ac.uk
rMLST database accession
113026
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
9 updates show details
date entered
2015-03-17
datestamp
2020-04-16

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
193
total length
2,133,479 bp
max length
168,641 bp
mean length
11,055 bp
N50 contig number
16
N50 length (L50)
40,965
N90 contig number
58
N90 length (L90)
9,982
N95 contig number
71
N95 length (L95)
6,202
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: 108 (39 isolates)

Schemes and loci

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