Detection of selective sweeps in cattle using genome-wide SNP data

Ramey, Holly R; Decker, Jared E; McKay, Stephanie D; Rolf, Megan M; Schnabel, Robert D; Taylor, Jeremy F

doi:10.1186/1471-2164-14-382

BMC Genomics

Table 3 Putative breed-specific selective sweeps identified using the AFFXB1P data

From: Detection of selective sweeps in cattle using genome-wide SNP data

Breed	BTA	UMD3.1 coordinates (bp)	Size (bp)	# Total SNP	# Fixed SNP	# Variable SNP
Angus	1	1,673,108-2,024,737	351,629	235	231	4
	1	111,659,758-111,900,241	240,483	231	221	10
	3	28,196,188-28,405,853	209,665	207	199	8
	6	6,308,164-6,696,861	388,697	74	72	2
	8	70,780,263-71,227,757	447,494	24	24	0
	8	73,538,014-73,760,303	222,289	288	282	6
	11	99,717,097-99,929,710	212,613	63	60	3
	14	3,550,689-3,885,375	334,686	21	21	0
	14	24,631,146-25,173,007	541,861	387	376	11
	18	200,903-406,270	205,367	117	114	3
	20	70,827,025-71,040,113	213,088	30	29	1
	21	1,186,567-1,489,860	303,293	26	25	1
	21	3,091,822-3,417,143	325,321	308	301	7
	25	39,262,249-39,468,067	205,818	21	20	1
	27	36,633,324-36,896,534	263,210	135	130	5
	29	49,557,166-49,922,377	365,211	70	69	1
Brahman	5	48,679,627-48,903,409	223,782	249	237	12
	10	24,519,718-24,794,435	274,717	20	20	0
	22	10,701,509-10,963,520	262,011	88	86	2
Hanwoo	9	1,384,189-1,586,988	202,799	214	211	3
	22	60,772,158-61,015,491	243,333	24	23	1
Simmental	1	83,467,837-83,685,705	217,868	124	118	6
	2	36,576,839-36,828,533	251,694	216	206	10
	2	119,873,146-120,084,764	211,618	158	151	7
	2	121,398,894-121,698,563	299,669	196	188	8
	5	68,631,784-68,857,802	226,018	276	267	9
	7	21,101,050-21,348,345	247,295	65	63	2
	7	52,426,108-52,673,522	247,414	40	38	2
	8	70,246,437-70,540,424	293,987	163	158	5
	10	59,147,189-59,382,774	235,585	190	182	8
	10	72,811,087-73,041,092	230,005	217	210	7
	13	12,236,039-12,524,368	288,329	382	369	13
	13	66,468,866-66,708,674	239,808	153	146	7
	15	82,007,368-82,208,624	201,256	32	32	0
	16	42,555,966-42,788,613	232,647	46	44	2
	16	43,767,572-44,053,904	286,332	186	181	5
	17	13,291,922-13,492,010	200,088	141	136	5
	19	34,588,859-35,435,279	846,420	59	57	2
	22	2,788,408-3,001,597	213,189	216	214	2
	25	26,433,626-26,744,488	310,862	126	120	6
	25	42,202,212-42,775,697	573,485	21	21	0
	28	30,480,640-30,711,987	231,347	254	243	11
	29	39,045,837-39,396,761	350,924	93	91	2
	29	49,052,295-49,273,683	221,388	21	20	1
Wagyu	1	197,944-574,931	376,987	321	313	8
	1	12,544,028-12,840,164	296,136	335	325	10
	2	71,299,739-71,508,079	208,340	177	169	8
	2	136,434,039-136,676,537	242,498	22	21	1
	3	12,027,611-12,227,923	200,312	65	64	1
	3	113,841,208-114,151,444	310,236	189	181	8
	3	117,817,862-118,017,993	200,131	114	110	4
	4	117,846,325-118,095,397	249,072	21	20	1
	4	119,437,108-119,832,270	395,162	26	25	1
	11	33,020,266-33,264,604	244,338	307	293	14
	11	59,513,020-59,783,144	270,124	282	269	13
	11	103,333,722-103,590,033	256,311	33	32	1
	11	105,596,531-105,828,115	231,584	23	22	1
	12	23,283-377,340	354,057	137	137	0
	13	15,493,906-15,739,251	245,345	305	301	4
	13	58,016,490-58,335,951	319,461	114	110	4
	16	51,275,719-51,519,519	243,800	39	38	1
	19	53,829,568-54,065,288	235,720	25	24	1
	22	49,088,027-49,456,146	368,119	102	98	4
	24	36,584,702-36,795,576	210,874	224	218	6
	27	17,911,399-18,114,646	203,247	304	289	15

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ISSN: 1471-2164

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