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Table 2 Genome-wide identification of selective sweep regions with low diversity (π ≤ 0.0002) within each of the two subspecies, respectively, but with high divergence (D xy ≥0.002) between these two subspecies, which were defined as DR-I. Six regions showed slightly higher π values (≥0.0002 but ≤0.0003, flagged by * in this table) because these were merged regions (See methods)

From: Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars

  Chr Range of the blocks Length
(bp)
π Jap
*105
π Tro
*105
π Tem
*105
π Ind
*105
D Jap-Ind
*105
D Tro-Ind
*105
D Tmp-Ind
*105
π Wild
*105
D Jap-Wild
*105
D Ind-Wild
*105
1 chr01 35499730–35510003 10274 4 2 6 14 242 246 241 89 178 121
2* chr01 35839043–35890683 51641 19 10 13 21 468 478 467 232 320 263
3 chr02 13139975–13160003 20029 18 5 6 18 295 305 301 133 209 142
4 chr02 13349983–13360044 10062 13 2 4 11 241 249 246 101 149 131
5 chr02 14944936–14962544 17609 15 3 4 14 250 260 252 121 157 145
6 chr02 27708263–27721727 13465 11 4 11 14 263 271 263 87 143 145
7 chr03 1579192–1602557 23366 16 4 15 14 302 307 311 153 183 193
8* chr03 2483329–2542460 59132 16 20 9 25 434 444 435 198 275 239
9 chr03 2706518–2724355 17838 13 18 7 18 440 453 440 188 310 210
10 chr03 2832279–2854311 22033 3 3 4 16 304 310 306 214 210 243
11 chr03 2896026–2923841 27816 5 3 5 15 321 327 323 151 178 220
12* chr03 2997394–3195565 198172 18 11 22 21 578 590 580 260 356 316
13 chr03 3479756–3498823 19068 3 2 3 14 241 245 243 132 180 138
14* chr03 24189350–24230136 40787 20 14 28 22 504 511 508 289 341 306
15 chr03 28469725–28489493 19769 14 21 7 12 429 437 427 245 327 308
16 chr04 34409908–34420007 10100 13 6 15 19 314 316 319 159 216 176
17 chr04 34469603–34500654 31052 14 6 16 16 262 264 265 123 169 136
18* chr05 21659599–21670204 10606 16 7 25 21 289 295 291 156 177 202
19 chr05 22789981–22800012 10032 17 6 16 15 319 328 331 472 379 421
20 chr05 22869880–22880236 10357 6 2 3 17 295 305 302 137 155 208
21 chr05 24026607–24070766 44160 20 9 35 18 604 614 616 318 438 349
22 chr05 24300403–24330214 29812 16 8 13 11 343 356 350 348 346 329
23 chr05 26824033–26840483 16451 11 2 4 17 233 243 239 131 172 137
24 chr07 4149981–4163826 13846 9 8 2 18 214 220 217 420 365 365
25 chr07 25598750–25620217 21468 8 10 5 16 323 327 323 155 219 190
26 chr09 22759164–22771433 12270 6 1 3 18 251 258 254 171 164 204
27 chr09 22910542–22930021 19480 14 8 11 18 345 356 349 242 251 256
28* chr10 21289972–21400480 110509 18 10 12 23 517 534 521 250 336 263
Average 31829 13 7 11 17 344 352 347 203 247 227