Full information on isolate OX9931489 (id:4192)
Projects
This isolate is a member of the following project:
- UKMenCar1
- United Kingdom Meningococcal Carriage Study - 1999
Provenance/primary metadata
- id
- 4192
- isolate
- OX9931489
- strain designation
- C: P1.21,16: F5-1: ST-66 (cc8)
- alias
- Ox99_31489
- country
- UK [England]
- continent
- Europe
- town or city
- Oxford
- year
- 1999
- age yr
- 16
- age range
- 15-24
- sex
- female
- disease
- carrier
- source
- throat swab
- epidemiology
- carrier
- species
- Neisseria meningitidis
- serogroup
- NG
- genogroup
- C
- capsule group
- C
- serotype
- 2b
- comments
- Previous Sanger seq. MLST updated with WGS data as per Bratcher et al. BMC Genomics. 2014 18 15:1138; Study Centre: Oxford
Tracking
- bioproject accession
- PRJEB23790 www.ebi.ac.uk
- biosample accession
- SAMEA104416879; ERS2034821 www.ebi.ac.uk
- ENA run accession
- ERR2214152 www.ebi.ac.uk
- sender
- Ana-Belen Ibarz-Pavon, Centre de Recerca en Salut Internacional de Barcelona (CRESIB) & Centro de Investigacao em Saude da Manhica (CISM)
- curator
- James Bray, University of Oxford, UK (E-mail: james.bray@biology.ox.ac.uk)
- update history
- 48 updates show details
- date entered
- 2003-12-17
- datestamp
- 2023-06-07
Secondary metadata
Deduced vaccine reactivity
Risk factors
- UK school year
- 12
- persons in household
- 4
- antibiotic use
- no
- cigarettes per day
- 0
- passive smoking
- no
- pubs clubs per week
- 1
- persons kissed past week
- 0
Publication (1)
- Spinsanti M, Brignoli T, Bodini M, Fontana LE, De Chiara M, Biolchi A, Muzzi A, Scarlato V, Delany I (2021). Deconvolution of intergenic polymorphisms determining high expression of Factor H binding protein in meningococcus and their association with invasive disease. PLoS Pathog 17:e1009461
Sequence bin
- contigs
- 127
- total length
- 2,149,272 bp
- max length
- 239,705 bp
- mean length
- 16,924 bp
- N50
- 48,842
- L50
- 13
- N90
- 15,798
- L90
- 41
- N95
- 9,281
- L95
- 51
- %GC
- 51.72
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,153
Annotation quality metrics
Provenance information
Scheme completion
Scheme | Scheme loci | Designated loci | Annotation | |
---|---|---|---|---|
Score | Status | |||
rplF species | 1 | 1 | 100 | |
Finetyping antigens | 3 | 3 | 100 | |
Bexsero Antigen Sequence Typing (BAST) | 5 | 5 | 100 | |
MLST | 7 | 7 | 100 | |
Ribosomal MLST | 53 | 53 | 100 | |
N. meningitidis cgMLST v2 | 1422 | 1413 | 99 |
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
Experimental schemes are subject to change and are not a stable part of the nomenclature.
Classification scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
---|---|---|---|---|---|
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 696 (5560 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 796 (5553 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 917 (5532 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1134 (82 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1617 (62 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 29 (43 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 2281 (42 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 696 (5560 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 796 (5553 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 917 (5532 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1134 (82 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1617 (62 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 29 (43 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 2281 (42 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 292 (1 isolate) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 304 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 320 (1 isolate) |
Schemes and loci
- All loci
- Capsule
- Genetic Information Processing
- Genomic islands
- Lineage Schemes
- Metabolism
- Peptidoglycan Biosynthesis
- Pilin
- Typing
- Other schemes
- Loci not in schemes
Navigate and select schemes within tree to display allele designations
Tools
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