Scheme information - cgMLST
Core-genome based MLST typing scheme
Curator
This scheme is curated by:
- Mélanie Hennart, Institut Pasteur, France
Fields
The primary key field indexes unique combinations of alleles at the member loci.
- cgST Primary key
Loci
This scheme consists of alleles from 1305 loci.
Profiles
This scheme has 4,571 profiles defined.
LIN codes
This scheme has LIN codes defined. See Palma et al. bioRxiv 2024.03.11.584534.| Bin | Threshold (allelic differences) |
|---|---|
| 1 | 1240 |
| 2 | 1035 |
| 3 | 500 |
| 4 | 55 |
| 5 | 25 |
| 6 | 8 |
| 7 | 4 |
| 8 | 2 |
| 9 | 1 |
| 10 | 0 |
The following nickname fields have been defined. These are used to search specific LIN code prefixes using human-readable names.
| Field | Type |
|---|---|
| Species | text |
| Lineage | text |
| Sublineage | text |
| Clonal group | text |
| Genetic cluster | text |