Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel

Khatkar, Mehar S; Nicholas, Frank W; Collins, Andrew R; Zenger, Kyall R; Cavanagh, Julie AL; Barris, Wes; Schnabel, Robert D; Taylor, Jeremy F; Raadsma, Herman W

doi:10.1186/1471-2164-9-187

Table 1 Number of SNPs, mean minor allelic frequency (MAF), spacing between adjacent SNPs and estimated of LD on different autosomes in present study.

From: Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel

BTA	No. Snp	Mean MAF	Spacing (kb)	Mean D'	Median D'	Mean adj D'	Median adj D'	Swept radius based on D'	Mean r²	Median r²	Mean adj r²	Median adj r²
1	528	0.27	276	0.18	0.11	0.70	0.88	11993 (11514 – 12513)	0.013	0.003	0.337	0.107
2	462	0.30	270	0.18	0.11	0.70	0.87	8968 (8607 – 9360)	0.013	0.003	0.323	0.101
3	469	0.28	248	0.18	0.11	0.70	0.89	9307 (8996 – 9640)	0.014	0.003	0.309	0.096
4	384	0.29	284	0.18	0.12	0.66	0.81	9825 (9354 – 10346)	0.014	0.003	0.317	0.090
5	417	0.28	279	0.18	0.11	0.70	0.89	8945 (8623 – 9291)	0.014	0.003	0.316	0.109
6	443	0.28	252	0.18	0.11	0.70	0.92	10311 (9878 – 10784)	0.013	0.003	0.328	0.099
7	357	0.30	282	0.17	0.11	0.70	0.84	8883 (8564 – 9227)	0.015	0.003	0.303	0.118
8	389	0.29	265	0.19	0.12	0.68	0.89	15359 (14440 – 16403)	0.015	0.003	0.293	0.106
9	265	0.29	357	0.20	0.13	0.67	0.84	9109 (8579 – 9708)	0.018	0.004	0.330	0.086
10	403	0.29	238	0.19	0.12	0.68	0.85	7725 (7455 – 8016)	0.016	0.004	0.311	0.107
11	452	0.28	224	0.18	0.11	0.70	0.88	10830 (10453 – 11235)	0.013	0.003	0.312	0.099
12	276	0.28	278	0.19	0.12	0.69	0.90	7271 (6902 – 7683)	0.015	0.003	0.325	0.120
13	406	0.28	203	0.19	0.12	0.73	0.97	8919 (8633 – 9225)	0.017	0.003	0.382	0.165
14	303	0.30	271	0.20	0.13	0.72	0.94	7309 (7002 – 7643)	0.019	0.004	0.349	0.146
15	309	0.27	242	0.21	0.13	0.67	0.89	7530 (7156 – 7945)	0.017	0.004	0.336	0.100
16	317	0.30	230	0.19	0.13	0.71	0.91	5861 (5639 – 6102)	0.019	0.004	0.368	0.168
17	302	0.28	231	0.20	0.12	0.72	0.94	7788 (7503 – 8094)	0.018	0.004	0.319	0.126
18	294	0.30	212	0.19	0.12	0.66	0.86	7342 (7009 – 7708)	0.015	0.003	0.312	0.092
19	344	0.29	183	0.19	0.12	0.72	0.92	7500 (7240 – 7778)	0.016	0.003	0.290	0.118
20	254	0.27	265	0.21	0.14	0.68	0.82	10315 (9718 – 10990)	0.021	0.005	0.345	0.150
21	181	0.29	345	0.21	0.13	0.61	0.68	5273 (4923 – 5676)	0.019	0.004	0.234	0.064
22	252	0.29	230	0.21	0.14	0.72	0.91	7681 (7358 – 8033)	0.022	0.005	0.329	0.114
23	260	0.29	183	0.25	0.16	0.73	0.94	8610 (8197 – 9065)	0.024	0.006	0.318	0.117
24	222	0.29	271	0.21	0.14	0.65	0.80	5437 (5140 – 5770)	0.019	0.005	0.331	0.083
25	225	0.30	187	0.19	0.12	0.66	0.84	4417 (4187 – 4673)	0.019	0.004	0.308	0.097
26	184	0.27	255	0.24	0.17	0.71	0.90	7191 (6672 – 7797)	0.022	0.006	0.289	0.092
27	158	0.32	271	0.19	0.13	0.65	0.78	-	0.021	0.005	0.325	0.099
28	159	0.29	249	0.22	0.14	0.66	0.79	5916 (5474 – 6435)	0.020	0.005	0.288	0.068
29	180	0.30	250	0.21	0.13	0.67	0.85	4805 (4534 – 5110)	0.024	0.004	0.313	0.095
All	9195	0.29	252	0.19	0.12	0.69	0.88	8154 (8085 – 8225)	0.016	0.003	0.321	0.110

The values in the parentheses of swept radius are confidence interval of swept radius.
adj means estimate between adjacent SNPs only.

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