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Full information on isolate SMRU2948 (id:27572)

Provenance/primary metadata

id
27572
isolate
SMRU2948
country
Thailand
continent
Asia
region
Maela
year
2010
serotype
19F
diagnosis
carriage
host
human
source
nasopharynx
penicillin
0.125
ENA accession
ERR084174 www.ebi.ac.uk
rMLST database accession
82710
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
17 updates show details
date entered
2015-04-28
datestamp
2020-05-12

Publications (10)

  • Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ, Salter SJ, Harris D, Nosten F, Goldblatt D, Corander J, Parkhill J, Turner P, Bentley SD (2014). Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet 46:305-9
  • Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill J (2014). Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes. PLoS Genet 10:e1004547
  • Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP (2015). Selective and genetic constraints on pneumococcal serotype switching. PLoS Genet 11:e1005095
  • Gao CY, Cecconi F, Vulpiani A, Zhou HJ, Aurell E (2019). DCA for genome-wide epistasis analysis: the statistical genetics perspective. Phys Biol 16:026002
  • Haubold B, Klötzl F, Pfaffelhuber P (2015). andi: fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics 31:1169-75
  • Lees JA, Vehkala M, Välimäki N, Harris SR, Chewapreecha C, Croucher NJ, Marttinen P, Davies MR, Steer AC, Tong SY, Honkela A, Parkhill J, Bentley SD, Corander J (2016). Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nat Commun 7:12797
  • Lin M, Kussell E (2017). Correlated Mutations and Homologous Recombination Within Bacterial Populations. Genetics 205:891-917
  • Numminen E, Chewapreecha C, Sirén J, Turner C, Turner P, Bentley SD, Corander J (2014). Two-phase importance sampling for inference about transmission trees. Proc Biol Sci 281:20141324
  • 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
  • Skwark MJ, Croucher NJ, Puranen S, Chewapreecha C, Pesonen M, Xu YY, Turner P, Harris SR, Beres SB, Musser JM, Parkhill J, Bentley SD, Aurell E, Corander J (2017). Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis. PLoS Genet 13:e1006508

Sequence bin

contigs
194
total length
2,091,196 bp
max length
114,659 bp
mean length
10,780 bp
N50 contig number
16
N50 length (L50)
34,600
N90 contig number
64
N90 length (L90)
8,415
N95 contig number
82
N95 length (L95)
4,322
loci tagged
1,406
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: 1 (718 isolates)
Sp_cgc_400cgMLSTSingle-linkage400experimentalgroup: 1 (718 isolates)
Sp_cgc_300cgMLSTSingle-linkage300experimentalgroup: 1 (717 isolates)
Sp_cgc_200cgMLSTSingle-linkage200experimentalgroup: 1 (717 isolates)
Sp_cgc_100cgMLSTSingle-linkage100experimentalgroup: 238 (337 isolates)
Sp_cgc_50cgMLSTSingle-linkage50experimentalgroup: 307 (37 isolates)
Sp_cgc_25cgMLSTSingle-linkage25experimentalgroup: 389 (5 isolates)
Sp_cgc_10cgMLSTSingle-linkage10experimentalgroup: 539 (5 isolates)
Sp_cgc_5cgMLSTSingle-linkage5experimentalgroup: 684 (5 isolates)

Schemes and loci

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