Table 3 |
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|
Average Linkage Disequilibrium (r2) for different distances between closely located SNP pairs. |
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|
POP1 (40 k) |
POP2 (800 k) |
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|
|
|||||||
|
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) |
|
|
|
|||||||
|
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. |
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|
Brito et al. BMC Genetics 2011 12:80 doi:10.1186/1471-2156-12-80 |
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