Table 6.

Fold enrichment/depletion of SNPs in each annotation class for each trait in each breed

	3′ UTR variant	5′ UTR variant	Coding sequence variant	Downstream gene variant	Intergenic variant	Intron variant	Missense variant	Non-coding transcript	Splice acceptor variant	Splice region variant	Stop gained	Synonymous variant	Upstream gene variant
DHQ
AA	–	–	–	3.76	0.89	1.02	–	–	–	–	–	–	0.73
CH	3.40	0.46	–	1.08	1.09	0.84	0.62	–	–	–	7.12	0.97	0.39
HE	1.80	–	–	4.43	0.36	2.32	–	–	–	–	–	0.91	0.49
LM	1.30	0.85	–	0.50	1.02	1.09	1.15	–	–	0.67	12.89	0.47	0.37
SI	–	–	–	0.40	0.86	1.54	–	–	–	–	–	–	0.39
DL
AA	–	–	–	1.11	1.15	0.63	–	–	–	–	–	3.98	0.64
CH	7.36	–	–	2.10	0.96	1.00	0.72	1.60	–	–	18.71	1.07	0.50
HE	–	–	–	1.21	0.77	1.64	–	–	–	–	–	3.63	0.39
LM	2.33	–	–	0.20	1.25	0.58	–	–	79.49	–	–	–	0.19
SI	–	–	–	0.94	0.93	1.13	3.90	–	–	–	–	–	1.52
DIT
AA	–	–	–	0.14	1.03	1.12	–	–	–	–	–	–	0.66
CH	3.47	0.48	–	0.94	1.11	0.79	0.58	–	–	–	7.47	0.96	0.40
HE	–	–	–	0.40	0.48	2.43	2.49	–	–	–	–	–	0.98
LM	1.16	1.77	99.15	0.86	0.99	1.09	2.28	–	–	0.70	13.49	0.59	0.55
SI	–	–	–	0.86	1.04	1.05	–	–	–	–	–	–	0.62
TW
AA	–	–	–	0.64	1.19	0.64	–	–	–	–	–	2.91	0.31
CH	3.07	0.54	–	1.22	0.99	1.01	0.24	1.43	–	–	8.40	1.44	0.83
HE	–	–	–	1.10	0.87	1.50	–	–	–	–	–	–	–
LM	3.17	1.45	–	0.45	1.21	0.61	0.22	–	–	–	22.05	0.32	0.28
SI	2.10	9.65	–	3.62	0.55	1.26	0.74	–	–	23.85	–	–	5.36
WOW
AA	3.28	–	–	0.18	0.84	1.44	–	–	–	–	–	1.75	1.67
CH	6.90	–	–	1.16	1.00	1.00	–	–	–	–	27.28	1.09	0.60
HE	–	40.89	–	1.00	0.93	1.17	–	–	–	–	–	4.95	0.52
LM	2.15	2.46	–	0.58	1.12	0.84	0.37	–	–	–	–	0.32	0.41
SI	1.99	–	–	1.35	1.12	0.65	2.79	–	–	–	–	–	1.03