Full information on isolate GL9960287 (id:66032)
Projects
This isolate is a member of the following project:
- UKMenCar1
- United Kingdom Meningococcal Carriage Study - 1999
Provenance/primary metadata
- id
- 66032
- isolate
- GL9960287
- strain designation
- B: P1.7,ND: F1-5: ST-2631 (cc41/44)
- country
- UK [Scotland]
- continent
- Europe
- region
- South West
- year
- 1999
- age yr
- 17
- age range
- 15-24
- sex
- male
- disease
- carrier
- source
- throat swab
- epidemiology
- carrier
- species
- Neisseria meningitidis
- serogroup
- NG
- 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
- 21 updates show details
- date entered
- 2019-12-06
- datestamp
- 2023-05-19
Secondary metadata
Deduced vaccine reactivity
- Bexsero reactivity
- insufficient data notes
- Trumenba reactivity
- cross-reactive notes
- Trumenba notes
- fHbp_peptide: 19 is cross-reactive to vaccine variant - data derived from MEASURE assays (PMID:29535195), and SBA assays (PMID:22569484, PMID:22718089, PMID:22871351, PMID:23114369, PMID:23352429, PMID:26407272, PMID:26707218, PMID:26803328, PMID:26835974, PMID:26974889, PMID:27745812, PMID:27846061, PMID:28196734, PMID:28566335, PMID:29236639)
Risk factors
- UK school year
- 13
- persons in household
- 5
- antibiotic use
- no
- cigarettes per day
- 0
- passive smoking
- no
- pubs clubs per week
- 1
- persons kissed past week
- 1
Sequence bin
- contigs
- 104
- total length
- 2,131,597 bp
- max length
- 196,538 bp
- mean length
- 20,497 bp
- N50
- 60,427
- L50
- 11
- N90
- 15,511
- L90
- 34
- N95
- 9,538
- L95
- 42
- %GC
- 51.64
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,143
Annotation quality metrics
Provenance information
Scheme completion
Scheme | Scheme loci | Designated loci | Annotation | |
---|---|---|---|---|
Score | Status | |||
rplF species | 1 | 1 | 100 | |
Finetyping antigens | 3 | 2 | 66 | |
Bexsero Antigen Sequence Typing (BAST) | 5 | 3 | 60 | |
MLST | 7 | 7 | 100 | |
Ribosomal MLST | 53 | 53 | 100 | |
N. meningitidis cgMLST v2 | 1422 | 1417 | 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 | 698 (3944 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 799 (3364 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 921 (3015 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1445 (26 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 2014 (15 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 1408 (7 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 257 (2 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 289 (2 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 698 (3944 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 799 (3364 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 921 (3015 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1445 (26 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 2014 (15 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 1408 (7 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 257 (2 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 289 (2 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 14701 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 20642 (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
Export:
Analysis: