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Full information on isolate SA36 (id:33047)

Provenance/meta data

id
33047
isolate
SA36
country
South Africa
continent
Africa
year
2004
serotype
23F
age yr
69
diagnosis
meningitis
host
human
source
pleural fluid
penicillin
1
erythromycin
256
tetracycline
24
chloramphenicol
16
ENA accession
ERR016774 www.ebi.ac.uk
rMLST database accession
44800
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
16 updates show details
date entered
2016-07-13
datestamp
2020-04-02

Publications (4)

  • Bogaardt C, van Tonder AJ, Brueggemann AB (2015). Genomic analyses of pneumococci reveal a wide diversity of bacteriocins - including pneumocyclicin, a novel circular bacteriocin. BMC Genomics 16:554
  • Brueggemann AB, Harrold CL, Rezaei Javan R, van Tonder AJ, McDonnell AJ, Edwards BA (2017). Pneumococcal prophages are diverse, but not without structure or history. Sci Rep 7:42976
  • Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD (2011). Rapid pneumococcal evolution in response to clinical interventions. Science 331:430-4
  • 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
212
total length
2,166,961 bp
max length
82,184 bp
mean length
10,222 bp
N50 contig number
28
N50 length (L50)
23,915
N90 contig number
96
N90 length (L90)
6,394
N95 contig number
119
N95 length (L95)
3,814
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: 7 (4508 isolates)
Sp_cgc_500cgMLSTSingle-linkage500experimentalgroup: 2 (87 isolates)
Sp_cgc_400cgMLSTSingle-linkage400experimentalgroup: 2 (87 isolates)
Sp_cgc_300cgMLSTSingle-linkage300experimentalgroup: 2 (86 isolates)
Sp_cgc_200cgMLSTSingle-linkage200experimentalgroup: 2 (85 isolates)
Sp_cgc_100cgMLSTSingle-linkage100experimentalgroup: 2 (78 isolates)

Schemes and loci

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