Table 1. Homology measured by wgMLST and mapping approaches of potentially linked Campylobacter spp. isolates.
| Isolates* | CC | Sequence type | Variable loci | Raw SNPs† | Filtered SNPs‡ |
|---|---|---|---|---|---|
| 2-5/2-10 | ST-21 | ST-50 | 1 | 5 | 1 |
| 4-69/4-67 | ST-21 | ST-53 | 35 | 9 | 6 |
| 2-1/1-79 | ST-21 | ST-19 | 20 | 20 | 7 |
| 9-71/9-46 | ST-354 | ST-354 | 16 | 11 | 11 |
| 4-52/4-51 | ST-21 | ST-50 | 19 | 34 | 15 |
| 1-49/5-38 | ST-353 | ST-5 | 44 | 40 | 36 |
| 1-46/6-72 | ST-21 | ST-21 | 49 | 63 | 74 |
| 2-9/2-10 | ST-21 | ST-50 | 35 | 152 | 110 |
| 4-6/9-44 | ST-257 | ST-257 | 42 | 370 | 50 |
*Reads from isolates on the right were mapped against de novo assemblies of isolates on the left, based on the isolate that contained the fewest identified loci.
†Number of SNPs with a mapping and base quality of ≥30, depth of ≥8 and present in more than 90 % of reads.
‡Number of SNP after removal of likely recombinant regions.