Table 3.
Top SNPs and indels from PLINK GWAS association analysis between affected (clinical) and unaffected (non-clinical) tortoises
| Position | Gene | Type | Unadjusted P |
|---|---|---|---|
| SNPsa | |||
| NC_024232.1:1,105,959 | A. superbus venom factor 1-like | non-syn | 0.0001388 |
| NC_024232.1:1,105,940 | A. superbus venom factor 1-like | syn | 0.0001388 |
| NC_024232.1:1,105,284 | A. superbus venom factor 1-like | syn | 0.0001388 |
| NW_007281632.1:53,578 | Uncharacterized LOC101950941 | non-syn | 0.0001725 |
| NW_007281632.1:53,577 | Uncharacterized LOC101950941 | non-syn | 0.0001725 |
| Indelsb | |||
| NW_007281632.1:53,576 | Uncharacterized LOC101950941 | syn | 0.0001725 |
| NW_007281632.1:53,579 | Uncharacterized LOC101950941 | non-syn | 0.0001725 |
| NC_024234.1:2,112,869 | TNFRSF5-likec | syn | 0.0007433 |
Syn synonymous and non-syn non-synonymous
aAll of these SNPs had a false discovery rate of 0.4164 after correction for multiple tests
bAll of these indels had a false discovery rate of 0.2193 after correction for multiple tests
cTumor necrosis factor receptor superfamily member 5-like