Table 3.

Hardy Weinberg Equilibrium in WHWTs SNPs and indels are shown in 5’ to 3’ order top to bottom; 118 WHWT alleles counted for each marker with 100% call rate. Genotype frequencies are shown as homozygote for minor allele/heterozygote/homozygote for major allele. For significant deviation from Hardy Weinberg equilibrium the p value is highlighted in red

Marker	Minor Allele	Group	Genotype frequency	Observed Heterozygotes	Expected Heterozygotes	P value
SNP1	A	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP2	A	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP3	A	Case	0–0 - 28	0	0	1
		Control	0–0 - 31	0	0	1
SNP4	A	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP5	A	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP6	A	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP7	G	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP8	A	Case	0–0 - 28	0	0	1
		Control	0–0 - 31	0	0	1
SNP9	A	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP10	G	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP11	G	Case	0–0 - 28	0	0	1
		Control	0–0 - 31	0	0	1
SNP12	T	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP13	T	Case	0–3 - 25	0.107	0.101	1
		Control	0–1 - 30	0.032	0.032	1
SNP14	A	Case	7–11 - 10	0.393	0.494	0.275
		Control	9–15 - 7	0.484	0.498	1
SNP15	C	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP16	G	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP17	C	Case	0–0 - 28	0	0	1
		Control	0–0 - 31	0	0	1
SNP18	G	Case	7–12 - 9	0.429	0.497	0.466
		Control	5–12 - 14	0.387	0.458	0.438
SNP19	A	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
SNP20	T	Case	0–0 - 28	0	0	1
		Control	0–0 - 31	0	0	1
indel1	–	Case	0–0 - 28	0	0	1
		Control	0–0 - 31	0	0	1
indel2	–	Case	2–1 - 25	0.036	0.163	0.005
		Control	0–7 - 24	0.226	0.2	1
indel3	+	Case	2–4 - 22	0.143	0.245	0.066
		Control	0–8 - 23	0.258	0.225	1