Full information on isolate GL9960285 (id:66030)
Projects
This isolate is a member of the following project:
- UKMenCar1
- United Kingdom Meningococcal Carriage Study - 1999
Provenance/primary metadata
- id
- 66030
- isolate
- GL9960285
- strain designation
- B: P1.22,14: F1-7: ST-213 (cc213)
- country
- UK [Scotland]
- continent
- Europe
- region
- South West
- year
- 1999
- age yr
- 17
- age range
- 15-24
- sex
- female
- disease
- carrier
- source
- throat swab
- epidemiology
- carrier
- species
- Neisseria meningitidis
- serogroup
- B
- genogroup
- B
- genogroup notes
- B backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
- capsule group
- B
- comments
- Study Centre: Glasgow
Tracking
- date sampled
- 1999-12-07
- isoyear sampled
- 1999
- week sampled
- 49
- sender
- Holly Bratcher, University of Oxford
- curator
- Auto Tagger
- update history
- 20 updates show details
- date entered
- 2019-12-06
- datestamp
- 2023-05-19
Secondary metadata
Deduced vaccine reactivity
Risk factors
- UK school year
- 13
- persons in household
- 4
- antibiotic use
- no
- cigarettes per day
- 0
- passive smoking
- no
- persons kissed past week
- 1
Sequence bin
- contigs
- 174
- total length
- 2,247,433 bp
- max length
- 279,077 bp
- mean length
- 12,917 bp
- N50
- 51,010
- L50
- 10
- N90
- 11,095
- L90
- 40
- N95
- 4,096
- L95
- 55
- %GC
- 51.48
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,123
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 | 1419 | 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 | 735 (1286 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 839 (1259 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 969 (1199 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1181 (1051 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1940 (101 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 41 (922 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 735 (1286 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 839 (1259 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 969 (1199 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1181 (1051 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1940 (101 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 41 (922 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 5585 (1 isolate) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 10219 (1 isolate) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 14700 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 20641 (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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Analysis: