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

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

Position	Gene	Type	Unadjusted P
SNPs^a
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
Indels^b
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-like^c	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

ISSN: 1471-2164