Characteristics of linkage disequilibrium in North American Holsteins

BMC Genomics

Table 1 Pairwise linkage disequilibrium (r²) for syntetic SNPs at various distanced pooled over all autosomes

Distance	N	Mean	SD	Median	95% CI of the Mean		% (r² > 0.3)*	% (r² > 0.15)^#
0-40 kb	16,237	0.24	0.26	0.24	0.24	0.25	30	47
40-60 kb	12,683	0.20	0.23	0.19	0.19	0.20	23	40
60-100 kb	25,527	0.16	0.20	0.16	0.15	0.16	17	33
100-200 kb	62,422	0.11	0.15	0.11	0.11	0.12	10	24
200-500 kb	183,089	0.08	0.11	0.08	0.08	0.08	5	17
0.5-1 Mb	299,167	0.07	0.09	0.07	0.07	0.07	3	13
1-2 Mb	583,426	0.06	0.08	0.06	0.06	0.06	2	10
2-5 Mb	1,671,022	0.04	0.06	0.04	0.04	0.04	1	5
5-10 Mb	2,584,922	0.03	0.04	0.03	0.03	0.03	0	2
10-20 Mb	4,615,064	0.02	0.02	0.02	0.02	0.02	0	0
20-50 Mb	9,971,401	0.01	0.01	0.01	0.01	0.01	0	0
50-100 Mb	6,658,292	0.00	0.01	0.24	0.24	0.25	0	0
>100 Mb	988,416	0.00	0.00	0.19	0.19	0.20	0	0

*Percentage of pairs of SNPs with r²> 0.3, ^#Percentage of pairs of SNPs with r²> 0.15

ISSN: 1471-2164