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Full information on isolate VICE0539 (id:25311)

Provenance/primary metadata

id
25311
isolate
VICE0539
country
Iceland
continent
Europe
region
Reykjavík
year
2011
serotype
6A
age yr
1
diagnosis
otitis media
host
human
source
middle ear fluid
ENA accession
ERR540472 www.ebi.ac.uk
rMLST database accession
112996
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
10 updates show details
date entered
2015-03-17
datestamp
2020-04-03

Publication (1)

  • 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
242
total length
2,164,999 bp
max length
98,131 bp
mean length
8,947 bp
N50 contig number
21
N50 length (L50)
33,597
N90 contig number
70
N90 length (L90)
8,456
N95 contig number
89
N95 length (L95)
3,358
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)

Schemes and loci

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Tools

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