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Table 3 Top SNPs and indels from PLINK GWAS association analysis between affected (clinical) and unaffected (non-clinical) tortoises

From: Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations – a next generation sequencing approach in the gopher tortoise

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
  1. Syn synonymous and non-syn non-synonymous
  2. aAll of these SNPs had a false discovery rate of 0.4164 after correction for multiple tests
  3. bAll of these indels had a false discovery rate of 0.2193 after correction for multiple tests
  4. cTumor necrosis factor receptor superfamily member 5-like