Full information on isolate 901901 (id:43164)

Provenance/primary metadata

id
43164
isolate
901901
aliases
PRJEB8327; SAMEA3221783
country
USA
continent
North America
year
2006
serotype
11D
age yr
3
diagnosis
carriage
host
human
source
nasopharynx
ENA accession
ERR907534 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
11 updates show details
date entered
2019-03-25
datestamp
2020-05-13

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
70
total length
1,998,332 bp
max length
257,274 bp
mean length
28,548 bp
N50 contig number
8
N50 length (L50)
71,703
N90 contig number
25
N90 length (L90)
24,802
N95 contig number
30
N95 length (L95)
18,493
loci tagged
1,404

Show sequence bin

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: 3178 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Analysis: