Skip to main content

Table 4 Average Linkage Disequilibrium (r2) between adjacent SNPs pairs and distribution across different r2 ranges.

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

   Number of SNP Pairs and (%)
  LD (r2) range 0.10 0.25 0.40
POP1 (40 K) 0.00-0.10 975 (36.97) 1040 (38.35) 1060 (37.80)
  0.10-0.20 463 (17.56) 468 (17.26) 501 (17.87)
  0.20-0.30 305 (11.57) 316 (11.65) 331 (11.80)
  0.30-0.40 232 (8.80) 232 (8.55) 248 (8.84)
  0.40-0.50 192 (7.28) 195 (7.19) 182 (6.49)
  0.50-0.60 126 (4.78) 142 (5.24) 136 (4.85)
  0.60-0.70 110 (4.17) 98 (3.61) 107 (3.82)
  0.70-0.80 83 (3.15) 78 (2.88) 81 (2.89)
  0.80-0.90 62 (2.35) 66 (2.43) 79 (2.82)
  0.90-1.00 89 (3.38) 77 (2.84) 79 (2.82)
  Average LD (r2) 0.26 0.25 0.25
POP2 (800 K) 0.00-0.10 13980 (29.54) 14124 (29.71) 14939 (31.03)
  0.10-0.20 8034 (16.98) 7443 (15.66) 8072 (16.77)
  0.20-0.30 5388 (11.38) 5442 (11.45) 5571 (11.57)
  0.30-0.40 4149 (8.77) 4240 (8.92) 4156 (8.63)
  0.40-0.50 3250 (6.87) 3418 (7.19) 3321 (6.90)
  0.50-0.60 2859 (6.04) 2837 (5.97) 2665 (5.54)
  0.60-0.70 2359 (4.98) 2479 (5.21) 2274 (4.72)
  0.70-0.80 1928 (4.07) 2162 (4.55) 2121 (4.41)
  0.80-0.90 1929 (4.08) 2032 (4.27) 1924 (4.00)
  0.90-1.00 3451 (7.29) 3362 (7.07) 3095 (6.43)
  Average LD (r2) 0.33 0.33 0.32
  1. The results are for chromosome 1 in the recent generations for three heritability levels and POP1 (40 k) and POP2 (800 k) over 10 replicates.