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Full information on isolate 903801 (id:43296)

Provenance/primary metadata

id
43296
isolate
903801
aliases
PRJEB8327; SAMEA3221834
country
USA
continent
North America
year
2007
serotype
11D
diagnosis
carriage
host
human
source
nasopharynx
comments
Age 12-<24m
ENA accession
ERR907668 www.ebi.ac.uk
sender
Melissa Jansen van Rensburg
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
2019-03-25
datestamp
2020-04-08

Publication (1)

  • Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson CM, Bentley SD, O'Brien KL, Hanage WP, Lipsitch M (2018). The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome. PLoS Pathog 14:e1006966

Sequence bin

contigs
58
total length
1,999,496 bp
max length
269,307 bp
mean length
34,475 bp
N50 contig number
7
N50 length (L50)
72,869
N90 contig number
21
N90 length (L90)
31,295
N95 contig number
25
N95 length (L95)
20,106
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: 4 (309 isolates)
Sp_cgc_400cgMLSTSingle-linkage400experimentalgroup: 4 (231 isolates)
Sp_cgc_300cgMLSTSingle-linkage300experimentalgroup: 4 (231 isolates)
Sp_cgc_200cgMLSTSingle-linkage200experimentalgroup: 4 (230 isolates)
Sp_cgc_100cgMLSTSingle-linkage100experimentalgroup: 4 (123 isolates)
Sp_cgc_50cgMLSTSingle-linkage50experimentalgroup: 4 (25 isolates)
Sp_cgc_25cgMLSTSingle-linkage25experimentalgroup: 2097 (8 isolates)
Sp_cgc_10cgMLSTSingle-linkage10experimentalgroup: 3205 (4 isolates)
Sp_cgc_5cgMLSTSingle-linkage5experimentalgroup: 3847 (4 isolates)

Schemes and loci

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Tools

Analysis: