Table 1.
Characteristics of all amplicons used in genotyping assay. Detailed results for individual SNPs within all non-immune loci included in the final assay is provided in the Additional file 1: Tables S1 and S2
| Amplicon | Target variation | Chra | Length (bp) | No. of SNPs | No. of SNPs not in HWE | No. of haplotypes |
|---|---|---|---|---|---|---|
| AGA | Neutral | 6 | 9352 | 34 | 2 (6 %) | 2 |
| CCLD5/6b | Chemokine | 4 | 8209 | 25 | 22 (88 %) | 18 |
| CX3Cb | Chemokine | 1 | 9425 | 3 | 1 (33 %) | 6 |
| DIG12b | NK receptor | 3 | 6351 | 15 | 0 (0 %) | 3 |
| DIG24b | NK receptor | 3 | 6809 | 1 | 1 (100 %) | 2 |
| DRD5 | Dopamine receptor | 6 | 7885 | 1 | 0 (0 %) | 2 |
| ERN2 | Pro-apoptotic | 2 | 10,165 | 17 | 17 (100 %) | 2 |
| FOXA2 | Neutral | 1 | 10,122 | 39 | 4 (10 %) | 29 |
| IL17Bb | Interleukin | 1 | 5717 | 20 | 1 (5 %) | 2 |
| IL22F1b | Interleukin | 1 | 6531 | 3 | 2 (67 %) | 3 |
| KIT | Neutral | 2 | 8356 | 2 | 1 (50 %) | 3 |
| NF2 | Neutral | 2 | 9312 | 41 | 1 (2 %) | 3 |
| PLEKHM3 | Neutral | 3 | 10,034 | 16 | 2 (13 %) | 5 |
| RAB27A | Neutral | 1 | 10,077 | 2 | 0 (0 %) | 3 |
| TGFB1b | Cytokine | 3 | 2649 | 2 | 0 (0 %) | 3 |
| TLR3b | Toll-like receptor | 6 | 7663 | 32 | 4 (13 %) | 6 |
| UNC13B | Neutral | 2 | 9687 | 14 | 0 (0 %) | 3 |
| Total | 138,344 | 267 | 58 | 95 |
Nb. Amplicons are named according to nearest annotated gene: amplicons are not necessarily targeting the gene they are named for
aChromosome as indicated by Tasmanian devil reference genome v7.1 [32] however recent work has identified that chromosomes 1 and 2 were mis-identified [50]
bIndicates immune-targeted amplicon [40]