Full information on isolate 0232/93 (id:1622)
Provenance/primary metadata
- id
- 1622
- isolate
- 0232/93
- strain designation
- C: P1.18-1,34: F1-9: ST-100 ()
- country
- Czech Republic
- continent
- Europe
- region
- P
- year
- 1993
- age yr
- 21
- age range
- 15-24
- sex
- male
- disease
- carrier
- source
- throat swab
- epidemiology
- carrier
- species
- Neisseria meningitidis
- serogroup
- C
- genogroup
- C
- genogroup notes
- C backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
- capsule group
- C
- serotype
- 4
- sero subtype
- NST
Tracking
- ENA run accession
- ERR137101 www.ebi.ac.uk
- sender
- Pavla Křížová, Pavla Křížová and Keith Jolley
- curator
- Keith Jolley, University of Oxford, UK (E-mail: keith.jolley@biology.ox.ac.uk)
- update history
- 111 updates show details
- date entered
- 2007-03-29
- datestamp
- 2021-06-18
Secondary metadata
Vaccines
- Bexsero reactivity
- exact match
notes - Bexsero notes
- NHBA_peptide: 2 is exact match to vaccine variant - peptide sequence match (PMID:27521232)
- 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)
Publications (5)
Sequence bin
- contigs
- 174
- total length
- 2,160,358 bp
- max length
- 172,876 bp
- mean length
- 12,416 bp
- N50
- 43,220
- L50
- 15
- N90
- 9,768
- L90
- 53
- N95
- 5,568
- L95
- 68
- %GC
- 51.55
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,179
Annotation quality metrics
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 | 1415 | 99 |
Analysis
rMLST species identification
Rank | Taxon | Taxonomy | Support | Matches |
---|---|---|---|---|
SPECIES | Neisseria meningitidis | Proteobacteria > Betaproteobacteria > Neisseriales > Neisseriaceae > Neisseria > Neisseria meningitidis | 100% |
Analysis performed: 2021-04-30
Similar isolates (determined by classification schemes)
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_20 | Ribosomal MLST | Single-linkage | 20 | experimental | 169 (25820 isolates) |
Bact_rmlstc_10 | Ribosomal MLST | Single-linkage | 10 | experimental | 476 (3832 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 698 (3506 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 799 (2989 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 921 (2680 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1193 (438 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 2215 (5 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 116 (7 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 176 (5 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 198 (2 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 209 (2 isolates) |
Bact_rmlstc_20 | Ribosomal MLST | Single-linkage | 20 | experimental | 169 (25820 isolates) |
Bact_rmlstc_10 | Ribosomal MLST | Single-linkage | 10 | experimental | 476 (3832 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 698 (3506 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 799 (2989 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 921 (2680 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1193 (438 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 2215 (5 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 116 (7 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 176 (5 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 198 (2 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 209 (2 isolates) |
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: