Full information on isolate GL9960156 (id:66025)
Projects
This isolate is a member of the following project:
- UKMenCar1
- United Kingdom Meningococcal Carriage Study - 1999
Provenance/primary metadata
- id
- 66025
- isolate
- GL9960156
- strain designation
- B: P1.22,14: F5-5: ST-213 (cc213)
- country
- UK [Scotland]
- continent
- Europe
- region
- South West
- year
- 1999
- age yr
- 15
- age range
- 15-24
- sex
- male
- 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
- 21 updates show details
- date entered
- 2019-12-06
- datestamp
- 2023-05-19
Secondary metadata
Deduced vaccine reactivity
- Bexsero reactivity
- none notes
- Bexsero notes
- fHbp_peptide: 45 is not cross-reactive with vaccine variant - data derived from MATS assays (PMID:23414709, PMID:25630407, PMID:26686998, PMID:26950303, PMID:28366725, PMID:30592763); NHBA_peptide: 18 is not cross-reactive with vaccine variant - data derived from MATS assays (PMID:23414709, PMID:25630407, PMID:26686998, PMID:26950303, PMID:27355628, PMID:28366725, PMID:30135218, PMID:30592763); NadA_peptide is missing; PorA_VR2 is not variant 4
- Trumenba reactivity
- exact match notes
- Trumenba notes
- fHbp_peptide: 45 is exact match to vaccine variant - peptide sequence match (PMID:20619376)
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
Sequence bin
- contigs
- 161
- total length
- 2,236,813 bp
- max length
- 217,128 bp
- mean length
- 13,894 bp
- N50
- 54,764
- L50
- 11
- N90
- 10,607
- L90
- 42
- N95
- 4,823
- L95
- 57
- %GC
- 51.55
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,099
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 | 1421 | 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 (1284 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 839 (1257 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 969 (1197 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1181 (1049 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1674 (416 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 41 (918 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 380 (484 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 3014 (180 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 735 (1284 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 839 (1257 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 969 (1197 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1181 (1049 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1674 (416 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 41 (918 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 380 (484 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 3014 (180 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 14699 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 20640 (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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