PubMLST Database home Contents
Log in
Help

Full information on isolate 705401 (id:43398)

Provenance/primary metadata

id
43398
isolate
705401
aliases
PRJEB8327; SAMEA3221940
country
USA
continent
North America
year
2007
serotype
11D
age yr
4
diagnosis
carriage
host
human
source
nasopharynx
ENA accession
ERR907770 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
10 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
69
total length
1,997,816 bp
max length
268,867 bp
mean length
28,954 bp
N50 contig number
9
N50 length (L50)
66,589
N90 contig number
24
N90 length (L90)
26,103
N95 contig number
28
N95 length (L95)
19,905
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: 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: 2405 (2 isolates)
Sp_cgc_10cgMLSTSingle-linkage10experimentalgroup: 3274 (2 isolates)
Sp_cgc_5cgMLSTSingle-linkage5experimentalgroup: 3937 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Analysis: