Table 4

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

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


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.

Brito et al. BMC Genetics 2011 12:80   doi:10.1186/1471-2156-12-80

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