Full information on isolate M21 240025 (id:115345)
Projects
This isolate is a member of the following project:
- MRF Meningococcal Genome Library
-
The MRF Meningococcus Genome Library is a collaboration between Public Health England, the Scottish Haemophilus, Legionella, Meningococcus and Pneumococcus Reference (SHLMPR) Laboratory, The Wellcome Trust Sanger Institute and the University of Oxford, funded by the Meningitis Research Foundation.
Use of the MRF Genome Library data must be cited in any publication or presentation making use of it.
Provenance/primary metadata
- id
- 115345
- isolate
- M21 240025
- strain designation
- B: P1.12-1,16: F1-5: ST-485 (cc41/44)
- country
- UK [England]
- continent
- Europe
- town or city
- London
- year
- 2021
- epidemiological year
- 07/2020-06/2021
- disease
- invasive (unspecified/other)
- species
- Neisseria meningitidis
- serogroup
- B
- genogroup
- B
- genogroup notes
- B backbone: All essential capsule genes intact and present. Prediction code: https://github.com/ntopaz/characterize_neisseria_capsule.
- capsule group
- B
- type strain
- 0
Tracking
- bioproject accession
- PRJEB9481 www.ebi.ac.uk
- biosample accession
- SAMEA13635372; ERS11237220 www.ebi.ac.uk
- run accession
- ERR9389329 www.ebi.ac.uk
- sender
- Aiswarya Lekshmi, Public Health England
- curator
- Auto Tagger
- update history
- 107 updates show details
- date entered
- 2022-03-23
- datestamp
- 2024-12-13
Secondary metadata
Deduced vaccine reactivity
- 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: 4 is cross-reactive to vaccine variant - data derived from MEASURE assays (PMID:29535195), and SBA assays (PMID:27846061, PMID:29236639)
Sequence bin
- method
- Illumina
- contigs
- 176
- total length
- 2,130,629 bp
- max length
- 91,102 bp
- mean length
- 12,106 bp
- N50
- 25,728
- L50
- 24
- N90
- 6,025
- L90
- 82
- N95
- 3,822
- L95
- 104
- %GC
- 51.66
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,128
Annotation quality metrics
Provenance information
Missing field values for: 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 v3 | 1329 | 1314 | 98 | |
N. meningitidis cgMLST v2 | 1422 | 1407 | 98 |
Similar isolates (determined by LIN codes)
- Scheme
- N. meningitidis cgMLST v3
- LIN code
- 0_14_0_0_0_1_54_6_0_0_0_0_0_0
Prefix | Threshold | Matching isolates |
---|---|---|
0_14_0_0_0_1_54_6_0_0 | 7 | 1 |
0_14_0_0_0_1_54_6_0_0_0 | 3 | 1 |
0_14_0_0_0_1_54_6_0_0_0_0 | 2 | 1 |
0_14_0_0_0_1_54_6_0_0_0_0_0 | 1 | 1 |
0_14_0_0_0_1_54_6_0_0_0_0_0_0 | 0 | 1 |
0 | 1218 | 37672 |
0_14 | 970 | 6314 |
0_14_0 | 691 | 5419 |
0_14_0_0 | 545 | 3224 |
0_14_0_0_0 | 385 | 3185 |
0_14_0_0_0_1 | 279 | 2851 |
0_14_0_0_0_1_54 | 156 | 389 |
0_14_0_0_0_1_54_6 | 67 | 1 |
0_14_0_0_0_1_54_6_0 | 14 | 1 |
0_14_0_0_0_1_54_6_0_0 | 7 | 1 |
0_14_0_0_0_1_54_6_0_0_0 | 3 | 1 |
0_14_0_0_0_1_54_6_0_0_0_0 | 2 | 1 |
0_14_0_0_0_1_54_6_0_0_0_0_0 | 1 | 1 |
0_14_0_0_0_1_54_6_0_0_0_0_0_0 | 0 | 1 |
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 | 698 (5147 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 799 (4359 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 921 (4009 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1173 (2134 isolates) |
Nm_cgc3_200 | N. meningitidis cgMLST v3 | Single-linkage | 200 | experimental | 38 (2584 isolates) |
Nm_cgc3_100 | N. meningitidis cgMLST v3 | Single-linkage | 100 | experimental | 506 (385 isolates) |
Bact_rmlstc_5 | Ribosomal MLST | Single-linkage | 5 | experimental | 698 (5147 isolates) |
Bact_rmlstc_4 | Ribosomal MLST | Single-linkage | 4 | experimental | 799 (4359 isolates) |
Bact_rmlstc_3 | Ribosomal MLST | Single-linkage | 3 | experimental | 921 (4009 isolates) |
Bact_rmlstc_2 | Ribosomal MLST | Single-linkage | 2 | experimental | 1173 (2134 isolates) |
Bact_rmlstc_1 | Ribosomal MLST | Single-linkage | 1 | experimental | 113482 (1 isolate) |
Nm_cgc3_200 | N. meningitidis cgMLST v3 | Single-linkage | 200 | experimental | 38 (2584 isolates) |
Nm_cgc3_100 | N. meningitidis cgMLST v3 | Single-linkage | 100 | experimental | 506 (385 isolates) |
Nm_cgc3_50 | N. meningitidis cgMLST v3 | Single-linkage | 50 | experimental | 14477 (1 isolate) |
Nm_cgc3_25 | N. meningitidis cgMLST v3 | Single-linkage | 25 | experimental | 19424 (1 isolate) |
Nm_cgc3_10 | N. meningitidis cgMLST v3 | Single-linkage | 10 | experimental | 25655 (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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Analysis: