Scheme information - scgMLST629_S
please cite
An update of scheme scgMLST initially identified in Bialek-Davenet et al, 2014. This 629-loci scheme is described in Hennart et al, 2022.
References
- Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022). A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Mol Biol Evol 39:
Curators
This scheme is curated by:
- Chiara Crestani, Pasteur Institute, France
- Federica Palma, Institut Pasteur, Paris, France
Fields
The primary key field indexes unique combinations of alleles at the member loci.
- scgST Primary key
Loci
This scheme consists of alleles from 629 loci.
Profiles
This scheme has 78,423 profiles defined.
LIN codes
This scheme has LIN codes defined. See Palma et al. bioRxiv 2024.03.11.584534.| Bin | Threshold (allelic differences) |
|---|---|
| 1 | 610 |
| 2 | 585 |
| 3 | 190 |
| 4 | 43 |
| 5 | 10 |
| 6 | 7 |
| 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 |
|---|---|
| Phylogroup | text |
| Sublineage | text |
| Clonal group | text |