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Table 3 Average Linkage Disequilibrium (r2) for different distances between closely located SNP pairs.

From: Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle

   POP1 (40 k) POP2 (800 k)
h2 Distance
range (Mb)
Pairs r2(SD) Frequency
r2 > 0.30 (%)
Pairs r2 (SD) Frequency
r2 > 0.30 (%)
  0.00-0.10 5049 0.23 (0.24) 1512 (29.95) 4275 0.24 (0.25) 1272 (29.75)
  0.10-0.20 5074 0.17 (0.19) 1063 (20.95) 4474 0.18 (0.20) 919 (20.54)
  0.20-0.30 6265 0.14 (0.16) 885 (14.13) 4290 0.14 (0.16) 644 (15.01)
  0.30-0.40 4938 0.12 (0.14) 510 (10.33) 4358 0.12 (0.14) 493 (11.31)
  0.40-0.50 5042 0.10 (0.13) 425 (8.43) 4280 0.10 (0.13) 359 (8.39)
0.10 0.50-0.60 6199 0.09 (0.11) 370 (5.97) 4196 0.09 (0.12) 279 (6.65)
  0.60-0.70 4994 0.08 (0.10) 228 (4.57) 4208 0.09 (0.11) 242 (5.75)
  0.70-0.80 5975 0.07 (0.09) 187 (3.69) 4268 0.08 (0.10) 190 (4.45)
  0.80-0.90 6183 0.07 (0.09) 167 (2.70) 4334 0.07 (0.10) 170 (3.92)
  0.90-1.00 4917 0.06 (0.08) 128 (2.60) 4163 0.07 (0.09) 149 (3.58)
  Overall 3932610 0.008 (0.03) 6151 (0.16) 3126250 0.01 (0.03) 6062 (0.19)
  0.00-0.10 5248 0.22 (0.24) 1495 (28.49) 4494 0.24 (0.25) 1375 (30.60)
  0.10-0.20 5224 0.17 (0.19) 1077 (20.62) 4740 0.18 (0.20) 1006 (21.22)
  0.20-0.30 6528 0.13 (0.16) 855 (13.10) 4630 0.14 (0.17) 724 (15.64)
  0.30-0.40 5147 0.11 (0.14) 461 (8.96) 4560 0.12 (0.14) 488 (10.70)
  0.40-0.50 5112 0.09 (0.12) 315 (6.16) 4596 0.11 (0.13) 406 (8.83)
0.25 0.50-0.60 6466 0.08 (0.11) 343 (5.31) 4469 0.10 (0.12) 333 (7.45)
  0.60-0.70 5146 0.07 (0.09) 186 (3.61) 4418 0.09 (0.11) 250 (5.66)
  0.70-0.80 5227 0.07 (0.09) 139 (2.66) 4502 0.08 (0.10) 226 (5.02)
  0.80-0.90 6431 0.06 (0.08) 178 (2.77) 4359 0.08 (0.10) 207 (4.75)
  0.90-1.00 5129 0.06 (0.08) 95 (1.85) 4416 0.07 (0.09) 154 (3.49)
  Overall 4096952 0.006 (0.03) 5689 (0.14) 3283438 0.011 (0.03) 6543 (0.20)
  0.00-0.10 5439 0.22 (0.24) 1517 (27.89) 4191 0.24 (0.24) 1265 (30.18)
  0.10-0.20 5468 0.17 (0.19) 1070 (19.57) 4225 0.17 (0.20) 865 (20.47)
  0.20-0.30 6801 0.13 (0.16) 886 (13.03) 4263 0.14 (0.16) 621 (14.57)
  0.30-0.40 5435 0.11 (0.14) 543 (9.99) 4251 0.12 (0.14) 457 (10.75)
  0.40-0.50 5444 0.09 (0.12) 361 (6.63) 4286 0.10 (0.12) 333 (7.77)
0.40 0.50-0.60 6782 0.08 (0.10) 293 (4.32) 4284 0.09 (0.11) 270 (6.30)
  0.60-0.70 5377 0.07 (0.09) 176 (3.27) 4103 0.09 (0.11) 232 (5.65)
  0.70-0.80 5374 0.07 (0.09) 150 (2.79) 4260 0.08 (0.10) 205 (4.81)
  0.80-0.90 6733 0.06 (0.08) 155 (2.30) 4285 0.07 (0.09) 136 (3.17)
  0.90-1.00 5342 0.06 (0.07) 75 (1.40) 4199 0.06 (0.08) 104 (2.48)
  Overall 4290985 0.006 (0.03) 5710 (0.13) 3072154 0.010 (0.03) 5305 (0.17)
  1. The results are for chromosome 1 in the recent generations for three heritability levels and POP1 (40 k) and POP2 (800 k) for one replicate. For POP2 (800 k), 40 k markers were randomly sampled to represent the 800 k panel.