Full information on isolate H10-EMI-009 (id:128314)
Provenance/primary metadata
- id
- 128314
- isolate
- H10-EMI-009
- strain designation
- Y: P1.5-1,10-1: F2-9: ST-14974 (cc92)
- country
- Spain
- continent
- Europe
- region
- Cantabria
- disease
- invasive (unspecified/other)
- 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
- sender
- Juanjo Gonzalez-López, Hospital Universitari Vall d'Hebron
- curator
- Auto Tagger
- update history
- 12 updates show details
- date entered
- 2023-03-30
- datestamp
- 2023-05-21
Secondary metadata
Deduced vaccine reactivity
- Bexsero reactivity
- none notes
- Bexsero notes
- fHbp_peptide: 21 is not cross-reactive with vaccine variant - data derived from MATS assays (PMID:23414709, PMID:26950303, PMID:27355628, PMID:28366725, PMID:29152576, PMID:30592763); NHBA_peptide: 9 is not cross-reactive with vaccine variant - data derived from MATS assays (PMID:26950303, PMID:30592763); NadA_peptide is missing; PorA_VR2 is not variant 4
- Trumenba reactivity
- cross-reactive notes
- Trumenba notes
- fHbp_peptide: 21 is cross-reactive to vaccine variant - data derived from SBA assays (PMID:27846061, PMID:29236639)
Sequence bin
- contigs
- 239
- total length
- 2,099,450 bp
- max length
- 203,996 bp
- mean length
- 8,785 bp
- N50
- 39,172
- L50
- 15
- N90
- 7,745
- L90
- 53
- N95
- 4,698
- L95
- 69
- %GC
- 51.70
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,061
Annotation quality metrics
Provenance information
Missing field values for: year, age_range, source
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 | 1397 | 98 |
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 | 903 (27 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 1029 (24 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 1194 (19 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1481 (9 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 2067 (2 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 903 (27 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 1029 (24 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 1194 (19 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1481 (9 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 2067 (2 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 2137 (1 isolate) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 5727 (1 isolate) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 10503 (1 isolate) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 15106 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 21166 (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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