TABLE 6.

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

		3′ UTR variant	5′ UTR variant	Downstream gene variant	Intergenic variant	Intron variant	Missense variant	Missense variant and splice	Non-coding transcript	Splice region variant	Stop gained	Synonymous variant	Upstream gene variant
WH	AA	5.70	–	0.83	1.04	0.95	0.79	–	–	–	–	0.86	0.61
	CH	–	–	0.54	1.24	0.50	–	–	–	–	–	0.69	0.67
	HE	–	–	0.23	1.25	0.54	0.71	–	–	–	–	0.52	0.45
	LM	0.21	–	0.53	1.28	0.39	–	–	1.29	0.66	–	0.54	0.79
	SI	1.11	–	0.31	1.10	0.92	0.78	–	–	–	–	1.14	0.37
	HF	4.41	–	3.20	0.93	0.82	2.32	–	–	–	–	1.68	1.37
BL	AA	–	–	0.53	1.09	0.87	1.65	–	–	–	–	0.80	0.77
	CH	2.94	0.41	1.21	1.00	1.04	0.43	–	–	–	6.35	1.18	0.41
	HE	3.80	4.37	1.22	1.02	0.91	1.97	–	–	–	68.90	0.48	0.82
	LM	–	1.26	0.58	1.26	0.44	0.95	7.85	1.67	0.85	–	0.42	0.72
	SI	–	–	1.09	0.76	1.56	2.70	–	–	–	135.73	0.99	1.16
CW	AA	–	–	1.11	0.99	1.12	–	–	–	–	–	1.11	0.36
	CH	–	5.66	1.33	0.87	1.36	1.71	–	–	–	–	1.90	0.41
	HE	1.20	–	2.22	1.16	0.46	–	–	–	–	–	0.61	0.98
	LM	–	–	2.25	0.83	1.36	–	–	–	–	–	2.26	0.36
	SI	2.84	–	2.08	0.96	0.99	–	–	–	–	–	–	0.93
	HF	–	–	3.85	1.09	0.44	–	–	–	–	–	–	1.06
CD	AA	–	–	1.15	0.82	1.41	1.43	–	12.15	9.56	–	6.21	0.56
	CH	–	–	1.23	0.96	0.96	–	–	–	–	–	1.39	2.08
	HE	–	–	1.11	1.21	0.46	–	–	9.67	–	–	0.83	0.98
	LM	–	–	0.39	1.31	0.39	–	–	–	–	–	0.54	0.29
	SI	–	–	0.77	1.20	0.51	1.07	–	–	–	–	2.34	1.00
HW	AA	3.31	–	0.28	1.01	1.10	–	–	–	–	–	3.32	0.36
	CH	2.96	–	1.00	0.92	1.20	–	–	–	–	–	1.50	1.13
	HE	1.78	–	0.30	1.18	0.53	1.23	–	–	–	–	1.81	1.64
	LM	1.54	–	0.50	1.30	0.38	–	–	–	1.19	–	0.20	0.40
	SI	3.01	–	1.19	0.79	1.53	–	–	–	–	–	–	0.99
	HF	–	–	1.68	1.05	0.59	–	–	29.22	–	–	–	2.44

AA, Angus; CH, Charolais; HE, Hereford; LM, Limousin; SE, Simmental; HF, Holstein-Friesian.