Full information on isolate H10-EMI-004 (id:128311)
Provenance/primary metadata
- id
- 128311
- isolate
- H10-EMI-004
- strain designation
- C: P1.5,2: F3-3: ST-11 (cc11)
- country
- Spain
- continent
- Europe
- region
- Cantabria
- disease
- invasive (unspecified/other)
- species
- Neisseria meningitidis
- genogroup
- C
- genogroup notes
- C backbone: internal stop in ctrA. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
- capsule group
- C
Tracking
- sender
- Juanjo Gonzalez-López, Hospital Universitari Vall d'Hebron
- curator
- Auto Tagger
- update history
- 11 updates show details
- date entered
- 2023-03-30
- datestamp
- 2023-05-20
Secondary metadata
Sequence bin
- contigs
- 236
- total length
- 2,119,414 bp
- max length
- 156,931 bp
- mean length
- 8,981 bp
- N50
- 38,085
- L50
- 17
- N90
- 9,162
- L90
- 59
- N95
- 5,170
- L95
- 74
- %GC
- 51.91
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,173
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 | 1419 | 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 | 696 (5553 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 796 (5546 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 917 (5525 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1121 (5391 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1599 (5282 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 156 (6900 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 540 (546 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 644 (454 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 696 (5553 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 796 (5546 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 917 (5525 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1121 (5391 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 1599 (5282 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 156 (6900 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 540 (546 isolates) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 644 (454 isolates) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 14703 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 20644 (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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