Full information on isolate MenAfriCar7061595 (id:120907)
Projects
This isolate is a member of the following project:
- MenAfriCar
- The African Meningococcal Carriage (MenAfriCar) consortium was established in 2009 to investigate the pattern of meningococcal carriage in countries of the African meningitis belt prior to and after the introduction of meningococcal serogroup A polysaccharide/tetanus toxoid conjugate vaccine.
Provenance/primary metadata
- id
- 120907
- isolate
- MenAfriCar7061595
- strain designation
- Y: P1.5-1,10-8: F1-3: ST-2880 (cc167)
- aliases
- 10.0-13280.0-XS3-722; 10-13280-XS3-1
- country
- Senegal
- continent
- Africa
- year
- 2012
- sex
- male
- disease
- carrier
- source
- throat swab
- epidemiology
- carrier
- species
- Neisseria meningitidis
- genogroup
- Y
- genogroup notes
- Y backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
- capsule group
- Y
Tracking
- date sampled
- 2012-04-13
- isoyear sampled
- 2012
- week sampled
- 15
- bioproject accession
- ERP024462 www.ebi.ac.uk
- biosample accession
- ERS4395873 www.ebi.ac.uk
- ENA run accession
- ERR4162230 www.ebi.ac.uk
- sender
- Neil MacAlasdair, WSI/University of Oslo
- curator
- Auto Tagger
- update history
- 15 updates show details
- date entered
- 2022-09-27
- datestamp
- 2023-05-19
Secondary metadata
Sequence bin
- contigs
- 78
- total length
- 2,150,960 bp
- max length
- 200,185 bp
- mean length
- 27,577 bp
- N50
- 62,375
- L50
- 12
- N90
- 21,434
- L90
- 34
- N95
- 11,911
- L95
- 41
- %GC
- 51.65
- Ns
- 21
- gaps
- 5
- loci tagged
- 2,128
Annotation quality metrics
Provenance information
Missing field values for: age_range
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)
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 | 703 (880 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 904 (565 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 1048 (118 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1289 (118 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 20005 (43 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 340 (99 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 2640 (49 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 8756 (11 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 12672 (5 isolates) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 18070 (2 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 703 (880 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 904 (565 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 1048 (118 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1289 (118 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 20005 (43 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 340 (99 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 2640 (49 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 8756 (11 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 12672 (5 isolates) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 18070 (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: