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Full information on isolate SMRU839 (id:27585)

Provenance/primary metadata

id
27585
isolate
SMRU839
country
Thailand
continent
Asia
region
Maela
year
2008
serotype
19F
diagnosis
carriage
host
human
source
nasopharynx
penicillin
0.5
ENA accession
ERR056705 www.ebi.ac.uk
rMLST database accession
83345
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
12 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
243
total length
2,043,880 bp
max length
80,422 bp
mean length
8,412 bp
N50 contig number
27
N50 length (L50)
22,381
N90 contig number
97
N90 length (L90)
5,195
N95 contig number
120
N95 length (L95)
3,192
loci tagged
1,410
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: 394 (10 isolates)
Sp_cgc_10cgMLSTSingle-linkage10experimentalgroup: 548 (6 isolates)
Sp_cgc_5cgMLSTSingle-linkage5experimentalgroup: 693 (3 isolates)

Schemes and loci

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