Full information on isolate NME15-009 (id:128309)
Provenance/primary metadata
- id
- 128309
- isolate
- NME15-009
- strain designation
- cnl: P1.18,25: F5-70: ST-17514 (cc198)
- country
- China
- continent
- Asia
- region
- Zhejiang
- town or city
- Hangzhou
- year
- 2015
- disease
- carrier
- source
- throat swab
- species
- Neisseria meningitidis
- serogroup
- NG
- genogroup
- cnl
- genogroup notes
- capsule null locus (cnl). Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
- capsule group
- cnl
Tracking
- sender
- Mark Renton, Hangzhou Center for Disease Control and Prevention
- curator
- Auto Tagger
- update history
- 12 updates show details
- date entered
- 2023-03-30
- datestamp
- 2023-05-21
Secondary metadata
Sequence bin
- contigs
- 295
- total length
- 2,062,572 bp
- max length
- 82,356 bp
- mean length
- 6,992 bp
- N50
- 17,712
- L50
- 38
- N90
- 4,997
- L90
- 115
- N95
- 2,627
- L95
- 143
- %GC
- 52.11
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,029
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 | 1398 | 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 | 900 (425 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 876 (119 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 1012 (114 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 21636 (14 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 28380 (14 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 1464 (6 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 900 (425 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 876 (119 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 1012 (114 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 21636 (14 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 28380 (14 isolates) |
Nm_cgc_200 | N. meningitidis cgMLST v2 | Single-linkage | 200 | experimental | 1464 (6 isolates) |
Nm_cgc_100 | N. meningitidis cgMLST v2 | Single-linkage | 100 | experimental | 5586 (1 isolate) |
Nm_cgc_50 | N. meningitidis cgMLST v2 | Single-linkage | 50 | experimental | 10220 (1 isolate) |
Nm_cgc_25 | N. meningitidis cgMLST v2 | Single-linkage | 25 | experimental | 14702 (1 isolate) |
Nm_cgc_10 | N. meningitidis cgMLST v2 | Single-linkage | 10 | experimental | 20643 (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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