Genetic Map in Mimulus species
P. A. Velasquez Vasconez
29 de mayo de 2017
Genetic Map in the Mimulus guttatus Species
As part of the homework of the class of Biometrics of Genetic Markers, offered by Dsc. Antonio Augusto Franco Garcia, ESALQ-USP, we constructed a genetic linkage map of an F2 population of an interespecific cross between M. guttatus and M. nasutus. For more details about this study see the originial article https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461909/pdf/11779808.pdf.
library(onemap)
fake_f2_onemap<-read_mapmaker(dir="C:/Users/alex/Desktop/bio",
file = "m_feb06.raw")## --Read the following data:
## Type of cross: f2
## Number of individuals: 287
## Number of markers: 418
## Missing trait values:
## fl: 11
## fs: 19
## ft: 11
## ll: 20
## nv: 12
## pa: 35
## pal: 11
## pv: 12
## sa: 11
## sl: 11
## ss: 28
## tl: 11
## tp: 12
## tw: 11
## vi: 12
## ww: 11str(fake_f2_onemap)#dados estrutura geral## List of 8
## $ geno : num [1:287, 1:418] 4 4 4 4 3 3 3 4 4 4 ...
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : NULL
## .. ..$ : chr [1:418] "AA461" "AA420" "AA404" "AA384" ...
## $ n.ind : num 287
## $ n.mar : num 418
## $ segr.type : chr [1:418] "C.A" "D.B" "C.A" "C.A" ...
## $ segr.type.num: num [1:418] 2 3 2 2 2 1 2 3 2 3 ...
## $ input : chr "C:/Users/alex/Desktop/bio/m_feb06.raw"
## $ n.phe : num 16
## $ pheno : num [1:287, 1:16] 20.6 17.8 18.1 13.5 15.1 ...
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : NULL
## .. ..$ : chr [1:16] "fl" "fs" "ft" "ll" ...
## - attr(*, "class")= chr [1:2] "onemap" "f2"plot(fake_f2_onemap)#The graphic is self-explanatory. ## No id variables; using all as measure variables
plot_by_segreg_type(fake_f2_onemap)
SEGREGATION TESTS
Now, it should be interesting to see if markers are segregating following what is expected by Mendel’s law.
f2_test <- test_segregation(fake_f2_onemap)
class(f2_test)## [1] "onemap_segreg_test"f2_testprint(f2_test)## Marker H0 Chi-square p-value % genot.
## 1 AA461 3:1 9.601212e+00 1.944490e-03 95.82
## 2 AA420 3:1 8.836364e-01 3.472076e-01 95.82
## 3 AA404 3:1 1.843636e+00 1.745253e-01 95.82
## 4 AA384 3:1 3.938182e+00 4.720177e-02 95.82
## 5 AA378 3:1 1.236485e+01 4.374931e-04 95.82
## 6 AA371C 1:2:1 5.392727e+00 6.745034e-02 95.82
## 7 AA361 3:1 4.810909e+00 2.828012e-02 95.82
## 8 AA341 3:1 2.241212e+00 1.343756e-01 95.82
## 9 AA311 3:1 5.441212e+00 1.966702e-02 95.82
## 10 AA280 3:1 3.404848e+00 6.500508e-02 95.82
## 11 AA277 3:1 3.503030e-01 5.539416e-01 95.82
## 12 AA270 3:1 5.441212e+00 1.966702e-02 95.82
## 13 AA268 3:1 1.484848e+00 2.230175e-01 95.82
## 14 AA246 3:1 1.090909e-02 9.168149e-01 95.82
## 15 AA208 3:1 9.818182e-02 7.540225e-01 95.82
## 16 AA173C 1:2:1 1.892000e+01 7.790659e-05 95.82
## 17 AA167 3:1 2.048485e-01 6.508354e-01 95.82
## 18 AA166C 1:2:1 3.296703e-02 9.836516e-01 95.12
## 19 AA163 3:1 8.757576e+00 3.083186e-03 95.82
## 20 AA158 3:1 1.212121e-03 9.722268e-01 95.82
## 21 AA137 3:1 1.387758e+01 1.951126e-04 95.82
## 22 AA100 3:1 5.441212e+00 1.966702e-02 95.82
## 23 AA95 3:1 7.575758e-01 3.840882e-01 95.82
## 24 AA66 3:1 5.939394e-02 8.074564e-01 95.82
## 25 BA497 3:1 8.901099e-01 3.454475e-01 95.12
## 26 BA449 3:1 1.011111e+01 1.473781e-03 95.12
## 27 BA445 3:1 4.250305e+00 3.924328e-02 95.12
## 28 BA416 3:1 1.397924e+01 1.848400e-04 95.12
## 29 BA400 3:1 4.407814e-01 5.067455e-01 95.12
## 30 BA394 3:1 5.813187e+00 1.590644e-02 95.12
## 31 BA387 3:1 2.496825e+01 5.828210e-07 95.12
## 32 BA384 3:1 9.890110e-02 7.531524e-01 95.12
## 33 BA374 3:1 8.010989e+00 4.649434e-03 95.12
## 34 BA372 3:1 8.901099e-01 3.454475e-01 95.12
## 35 BA334 3:1 1.026862e+00 3.108968e-01 95.12
## 36 BA314 3:1 1.173382e+00 2.787074e-01 95.12
## 37 BA311 3:1 1.495726e+00 2.213301e-01 95.12
## 38 BA301 3:1 2.697192e+00 1.005252e-01 95.12
## 39 BA222 3:1 2.063492e-01 6.496440e-01 95.12
## 40 BA220 3:1 6.155067e+00 1.310361e-02 95.12
## 41 BA214 3:1 2.567155e+01 4.047501e-07 95.12
## 42 BA210 3:1 4.846154e+00 2.770785e-02 95.12
## 43 BA196 3:1 2.933455e+01 6.089999e-08 95.12
## 44 BA175 3:1 5.813187e+00 1.590644e-02 95.12
## 45 BA172 3:1 5.982906e-02 8.067663e-01 95.12
## 46 BA158 3:1 2.257631e+00 1.329573e-01 95.12
## 47 BA153 3:1 1.450672e+01 1.396608e-04 95.12
## 48 BA145 3:1 8.901099e-01 3.454475e-01 95.12
## 49 BA129 3:1 1.729060e+01 3.207700e-05 95.12
## 50 BA125 3:1 4.846154e+00 2.770785e-02 95.12
## 51 BA117 3:1 1.098901e-02 9.165119e-01 95.12
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## 53 BA75 3:1 1.329670e+00 2.488639e-01 95.12
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## 55 BB327 3:1 1.784652e+01 2.394564e-05 96.86
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## 160 BA396C 1:2:1 9.904412e+00 7.067801e-03 94.77
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## 162 CA258C 1:2:1 1.410870e+01 8.636458e-04 96.17
## 163 CA389C 1:2:1 2.791304e+01 8.684796e-07 96.17
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## 167 AAT225 1:2:1 3.435510e+01 3.466446e-08 85.37
## 168 AAT261 1:2:1 1.156432e+01 3.082058e-03 83.97
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## 186 AAT300 1:2:1 1.692308e+00 4.290620e-01 72.47
## 187 CYCB 1:2:1 5.741036e+00 5.666957e-02 87.46
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## 253 CC338C 1:2:1 1.253061e+00 5.344428e-01 85.37
## 254 CC171C 1:2:1 4.560976e+00 1.022343e-01 85.71
## 255 AAT312 1:2:1 5.761905e+00 5.608133e-02 58.54
## 256 AAT283 1:2:1 1.061176e+01 4.962318e-03 59.23
## 257 LFY 1:2:1 4.300000e+00 1.164842e-01 83.62
## 258 AAT333 1:2:1 1.211732e+01 2.337533e-03 62.37
## 259 AP3 1:2:1 1.550943e+01 4.287155e-04 73.87
## 260 MgSTS17 1:2:1 1.118182e+01 3.731634e-03 91.99
## 261 MgSTS16 1:2:1 4.877477e+01 2.562667e-11 77.35
## 262 MgSTS18 1:2:1 5.403101e+00 6.710140e-02 89.90
## 263 MgSTS20 1:2:1 2.630566e+01 1.939985e-06 92.33
## 264 MgSTS21 1:2:1 1.095726e+01 4.175035e-03 81.53
## 265 MgSTS19 1:2:1 3.225984e+01 9.882440e-08 88.50
## 266 MgSTS24 1:2:1 3.481890e+01 2.748985e-08 88.50
## 267 MgSTS25 1:2:1 3.996226e+00 1.355909e-01 92.33
## 268 MgSTS22 1:2:1 2.360000e+00 3.072787e-01 95.82
## 269 MgSTS27 1:2:1 8.687732e+00 1.298622e-02 93.73
## 270 MgSTS26 1:2:1 1.088764e+01 4.322937e-03 93.03
## 271 MgSTS23 3:1 4.473358e-01 5.036029e-01 93.73
## 272 MgSTS28 1:2:1 1.405714e+01 8.861969e-04 97.56
## 273 MgSTS105 1:2:1 1.745247e+00 4.178538e-01 91.64
## 274 MgSTS120 1:2:1 2.551471e+00 2.792256e-01 94.77
## 275 MgSTS29 1:2:1 3.222936e+01 1.003423e-07 75.96
## 276 MgSTS38 1:2:1 1.955253e+01 5.678351e-05 89.55
## 277 MgSTS91 1:2:1 1.871642e+01 8.625445e-05 93.38
## 278 MgSTS93 1:2:1 1.628571e+01 2.908051e-04 92.68
## 279 MgSTS133 1:2:1 1.422963e+01 8.129712e-04 94.08
## 280 MgSTS58 1:2:1 3.362264e+00 1.861631e-01 92.33
## 281 MgSTS55 1:2:1 2.533333e+00 2.817693e-01 94.08
## 282 MgSTS40 1:2:1 5.156134e+00 7.592062e-02 93.73
## 283 MgSTS98 1:2:1 6.773438e+00 3.381947e-02 89.20
## 284 MgSTS45 1:2:1 1.200000e+01 2.478752e-03 93.38
## 285 MgSTS11 1:2:1 1.066935e+01 4.821465e-03 86.41
## 286 CYCA 1:2:1 7.848815e+01 9.047205e-18 73.52
## 287 aat356 1:2:1 8.664255e+01 1.533941e-19 81.88
## 288 MgSTS87 1:2:1 1.025313e+02 5.440289e-23 89.20
## 289 MgSTS132 1:2:1 1.645161e+00 4.392965e-01 86.41
## 290 MgSTS212 1:2:1 2.655738e+00 2.650415e-01 85.02
## 291 MgSTS228 1:2:1 6.853846e+00 3.248675e-02 90.59
## 292 MgSTS229 1:2:1 3.383459e+00 1.842007e-01 92.68
## 293 MgSTS234 1:2:1 9.381356e+00 9.180460e-03 82.23
## 294 MgSTS245 1:2:1 2.538710e+01 3.070874e-06 86.41
## 295 MgSTS308 1:2:1 1.016736e+00 6.014763e-01 83.28
## 296 MgSTS316 1:2:1 8.869565e-01 6.418002e-01 80.14
## 297 MgSTS323 1:2:1 5.236364e+00 7.293535e-02 76.66
## 298 MgSTS36 1:2:1 8.737052e+00 1.266990e-02 87.46
## 299 MgSTS43 1:2:1 3.481013e+00 1.754316e-01 82.58
## 300 MgSTS437 1:2:1 1.066923e+01 4.821764e-03 90.59
## 301 MgSTS48 1:2:1 6.739496e+00 3.439831e-02 82.93
## 302 MgSTS49 1:2:1 3.825000e+00 1.477106e-01 83.62
## 303 MgSTS59 1:2:1 8.692308e+00 1.295655e-02 81.53
## 304 MgSTS68 1:2:1 2.275862e+00 3.204814e-01 80.84
## 305 MgSTS70 1:2:1 2.430120e+01 5.285188e-06 86.76
## 306 MgSTS508 1:2:1 9.843137e-01 6.113065e-01 88.85
## 307 MgSTS527 1:2:1 5.127344e+01 7.347076e-12 89.20
## 308 MgSTS520 1:2:1 2.141107e+01 2.242053e-05 88.15
## 309 MgSTS529 1:2:1 2.781250e+00 2.489197e-01 89.20
## 310 MgSTS455 1:2:1 1.584746e+00 4.527692e-01 82.23
## 311 MgSTS468 1:2:1 4.483607e+00 1.062667e-01 85.02
## 312 MgSTS480 1:2:1 1.167939e+00 5.576803e-01 91.29
## 313 MgSTS474 1:2:1 6.666667e-02 9.672161e-01 88.85
## 314 MgSTS113 1:2:1 5.995745e+00 4.989311e-02 81.88
## 315 MgSTS106 1:2:1 2.062992e+00 3.564733e-01 88.50
## 316 MgSTS69 1:2:1 1.144355e+01 3.273897e-03 86.41
## 317 MgSTS56 1:2:1 2.927419e+00 2.313763e-01 86.41
## 318 MgSTS31 1:2:1 1.204918e+00 5.474638e-01 85.02
## 319 MgSTS95 1:2:1 1.115242e-02 9.944393e-01 93.73
## 320 MgSTS360 1:2:1 5.600415e+01 6.900070e-13 83.97
## 321 MgSTS262 1:2:1 3.137615e+00 2.082935e-01 75.96
## 322 MgSTS50 1:2:1 2.857820e+00 2.395699e-01 73.52
## 323 MgSTS75 1:2:1 2.188152e+01 1.772103e-05 73.52
## 324 MgSTS76 1:2:1 1.277228e+00 5.280238e-01 70.38
## 325 MgSTS341 1:2:1 2.353476e+01 7.753396e-06 65.16
## 326 MgSTS388 1:2:1 2.078341e+00 3.537480e-01 75.61
## 327 MgSTS330 1:2:1 2.188841e-01 8.963341e-01 81.18
## 328 MgSTS336 1:2:1 2.081481e+01 3.020789e-05 56.45
## 329 MgSTS332 1:2:1 1.614451e+01 3.120790e-04 60.28
## 330 MgSTS326 1:2:1 2.165217e+00 3.387108e-01 80.14
## 331 MgSTS282B 1:2:1 6.225806e+00 4.447166e-02 86.41
## 332 MgSTS282A 1:2:1 4.364807e+00 1.127702e-01 81.18
## 333 MgSTS255 1:2:1 2.870968e+00 2.380002e-01 86.41
## 334 MgSTS350 1:2:1 3.967213e+00 1.375722e-01 85.02
## 335 MgSTS348 1:2:1 2.462400e+01 4.497450e-06 87.11
## 336 MgSTS362 1:2:1 3.388186e+00 1.837659e-01 82.58
## 337 MgSTS358 1:2:1 4.129365e+01 1.079438e-09 87.80
## 338 MgSTS344 1:2:1 5.963563e+00 5.070243e-02 86.06
## 339 MgSTS471 1:2:1 6.378689e+01 1.408815e-14 63.76
## 340 MgSTS37 1:2:1 1.902954e+00 3.861703e-01 82.58
## 341 MgSTS34 1:2:1 4.777778e+00 9.173155e-02 84.67
## 342 MgSTS426 1:2:1 5.252336e+00 7.235518e-02 74.56
## 343 MgSTS453 1:2:1 5.073469e+00 7.912434e-02 85.37
## 344 MgSTS456 1:2:1 9.271493e+00 9.698863e-03 77.00
## 345 MgSTS457 1:2:1 4.439462e-01 8.009369e-01 77.70
## 346 MgSTS491 1:2:1 2.559740e+01 2.764360e-06 80.49
## 347 MgSTS492 1:2:1 3.904348e+00 1.419651e-01 80.14
## 348 MgSTS513 1:2:1 1.430380e+00 4.890992e-01 82.58
## 349 MgSTS509 1:2:1 6.892562e+00 3.186392e-02 84.32
## 350 MgSTS500 1:2:1 1.457627e+00 4.824811e-01 82.23
## 351 MgSTS430 1:2:1 2.863415e+00 2.389007e-01 71.43
## 352 MgSTS381 1:2:1 1.452991e-01 9.299266e-01 81.53
## 353 MgSTS398 1:2:1 6.949524e+01 8.115229e-16 73.17
## 354 MgSTS314 1:2:1 0.000000e+00 1.000000e+00 80.84
## 355 MgSTS380 1:2:1 1.049244e+02 1.644230e-23 82.93
## 356 MgSTS251 1:2:1 3.894410e+00 1.426723e-01 56.10
## 357 MgSTS351 1:2:1 1.062385e+01 4.932415e-03 75.96
## 358 MgSTS347 1:2:1 1.651685e+00 4.378658e-01 93.03
## 359 MgSTS320 1:2:1 1.620710e+01 3.024634e-04 58.89
## 360 MgSTS293 1:2:1 2.828358e+00 2.431251e-01 93.38
## 361 MgSTS263 1:2:1 3.205419e+01 1.095271e-07 70.73
## 362 MgSTS578 1:2:1 6.134454e-01 7.358546e-01 82.93
## 363 MgSTS571 1:2:1 9.609375e-01 6.184934e-01 89.20
## 364 MgSTS574B 1:2:1 7.079681e+00 2.901795e-02 87.46
## 365 MgSTS574a 1:2:1 1.051613e+01 5.205370e-03 86.41
## 366 MgSTS579 1:2:1 1.838095e+00 3.988988e-01 73.17
## 367 MgSTS638 1:2:1 5.733333e+00 5.688824e-02 83.62
## 368 MgSTS590 1:2:1 8.326996e-01 6.594495e-01 91.64
## 369 MgSTS589 1:2:1 1.469636e+00 4.795928e-01 86.06
## 370 MgSTS583 1:2:1 3.979412e+01 2.284637e-09 94.77
## 371 MgSTS586 1:2:1 1.337008e+01 1.249466e-03 88.50
## 372 MgSTS535 1:2:1 2.205882e-02 9.890312e-01 94.77
## 373 MgSTS537 1:2:1 6.092308e+00 4.754142e-02 90.59
## 374 MgSTS538 1:2:1 2.595420e-01 8.782965e-01 91.29
## 375 MgSTS536 1:2:1 1.609665e+00 4.471627e-01 93.73
## 376 MgSTS539 1:2:1 4.567164e+00 1.019185e-01 93.38
## 377 MgSTS631 1:2:1 2.152399e+01 2.118976e-05 94.43
## 378 MgSTS563 1:2:1 5.462094e+00 6.515105e-02 96.52
## 379 MgSTS562 1:2:1 7.378161e+01 9.517593e-17 90.94
## 380 MgSTS561 1:2:1 9.463296e+01 2.823021e-21 93.03
## 381 MgSTS558 1:2:1 1.074820e+01 4.635085e-03 96.86
## 382 MgSTS548 1:2:1 1.852632e+01 9.485531e-05 79.44
## 383 MgSTS419 1:2:1 1.230769e-01 9.403168e-01 90.59
## 384 MgSTS611 1:2:1 1.416058e+00 4.926141e-01 95.47
## 385 MgSTS632 1:2:1 7.826087e-01 6.761743e-01 96.17
## 386 MgSTS609 1:2:1 1.564286e+00 4.574248e-01 97.56
## 387 MgSTS600 1:2:1 9.175182e+00 1.017734e-02 95.47
## 388 MgSTS565 1:2:1 1.378182e+00 5.020323e-01 95.82
## 389 MgSTS606 1:2:1 9.960000e+00 6.874063e-03 95.82
## 390 MgSTS577 1:2:1 1.300730e+01 1.497962e-03 95.47
## 391 MgSTS425 1:2:1 1.951095e+01 5.797640e-05 95.47
## 392 MgSTS438 1:2:1 8.078740e+00 1.760856e-02 88.50
## 393 MgSTS435 1:2:1 2.829801e+01 7.164147e-07 52.61
## 394 MgSTS494 1:2:1 1.079892e+02 3.551672e-24 97.21
## 395 MgSTS477 1:2:1 1.908425e+00 3.851153e-01 95.12
## 396 MgSTS483 1:2:1 6.404317e+01 1.239377e-14 96.86
## 397 MgSTS383 1:2:1 5.168498e+00 7.545272e-02 95.12
## 398 MgSTS504A 1:2:1 3.579926e+00 1.669664e-01 93.73
## 399 MgSTS504B 1:2:1 7.711111e+00 2.116184e-02 94.08
## 400 MgSTS504C 1:2:1 1.133333e+00 5.674137e-01 94.08
## 401 MgSTS545 1:2:1 1.298851e+00 5.223459e-01 90.94
## 402 MgSTS542A 1:2:1 2.238462e+00 3.265309e-01 90.59
## 403 MgSTS542B 1:2:1 1.249027e+00 5.355218e-01 89.55
## 404 MgSTS598 1:2:1 7.442623e+00 2.420221e-02 85.02
## 405 MgSTS441 1:2:1 5.146667e+00 7.628085e-02 52.26
## 406 MgSTS620 1:2:1 4.080916e+01 1.375319e-09 91.29
## 407 MgSTS104 1:2:1 7.349057e+00 2.536137e-02 73.87
## 408 MgSTS511 1:2:1 4.258427e+00 1.189308e-01 93.03
## 409 MgSTS621 1:2:1 2.014925e-01 9.041624e-01 93.38
## 410 MgSTS622 1:2:1 1.635294e+00 4.414692e-01 88.85
## 411 MgSTS459 1:2:1 3.283582e-01 8.485900e-01 93.38
## 412 MgSTS220 1:2:1 2.977695e+00 2.256325e-01 93.73
## 413 MgSTS214 1:2:1 1.342205e+00 5.111446e-01 91.64
## 414 MgSTS467 1:2:1 8.253219e+00 1.613750e-02 81.18
## 415 MgSTS470 1:2:1 1.096887e+01 4.150876e-03 89.55
## 416 MgSTS599 1:2:1 1.429644e+01 7.862613e-04 88.15
## 417 MgSTS431 1:2:1 7.651376e+00 2.180343e-02 75.96
## 418 MgSTS440 1:2:1 1.064516e+00 5.872774e-01 86.41To guide you in the analysis, function Bonferroni shows the alpha value that should be considered for this number of loci if applying Bonferroni’s correction with global alpha of 0.05:
Bonferroni_alpha(f2_test)## [1] 0.0001196172plot(f2_test)
In this particular study, test was statistically significant, the 15% of the markers will be discarded. It is important to remember that Bonferroni’s correction is conservative. #list of markers with non-distorted segregation
(non_dist <- select_segreg(f2_test))## [1] "AA461" "AA420" "AA404" "AA384" "AA378"
## [6] "AA371C" "AA361" "AA341" "AA311" "AA280"
## [11] "AA277" "AA270" "AA268" "AA246" "AA208"
## [16] "AA167" "AA166C" "AA163" "AA158" "AA137"
## [21] "AA100" "AA95" "AA66" "BA497" "BA449"
## [26] "BA445" "BA416" "BA400" "BA394" "BA384"
## [31] "BA374" "BA372" "BA334" "BA314" "BA311"
## [36] "BA301" "BA222" "BA220" "BA210" "BA175"
## [41] "BA172" "BA158" "BA153" "BA145" "BA125"
## [46] "BA117" "BA113" "BA75" "BA69" "BB281"
## [51] "BB279" "BB259" "BB218" "BB216" "BB210"
## [56] "BB208" "BB198" "BB190" "BB186" "BB182"
## [61] "BB176" "BB167" "BB122" "BB119" "BB102"
## [66] "CA497" "CA415" "CA399" "CA392" "CA384"
## [71] "CA378" "CA315" "CA305" "CA297" "CA289"
## [76] "CA283" "CA279" "CA261" "CA238" "CA233"
## [81] "CA228" "CA220" "CA217" "CA210" "CA198"
## [86] "CA196" "CA174" "CA167" "CA152C" "CA150"
## [91] "CA140" "CA131" "CA122" "CA96" "CA75"
## [96] "CB333" "CB329" "CB309" "CB280" "CB272"
## [101] "CB257" "CB246" "CB230" "CB216" "CB187"
## [106] "CB173" "CB172" "CB166" "CB162" "CB156"
## [111] "CB126" "CB115" "CB55" "BD433" "BD429"
## [116] "BD411" "BD371" "BD316C" "BD292" "BD286"
## [121] "BD270" "BD263" "BD251" "BD243" "BD239"
## [126] "BD209" "BD179" "BD175" "BD170" "BD169"
## [131] "BD143" "BD130" "BD115" "BD99" "BD68"
## [136] "BD55" "BD189C" "AA153C" "AA296C" "AA346C"
## [141] "AA374C" "AA454C" "BA245C" "BA279C" "BA396C"
## [146] "CA183C" "CA258C" "CB263C" "BB103C" "AAT217"
## [151] "AAT261" "AAT240" "AAT278" "AAT39" "AAT211"
## [156] "AAT222" "AAT374" "AAT372" "AAT296" "AAT230"
## [161] "AAT308" "AG19" "AAT364" "AAT300" "CYCB"
## [166] "AAT242" "BC546" "BC542" "BC512" "BC506"
## [171] "BC498" "BC478" "BC392" "BC379" "BC376"
## [176] "BC374" "BC334" "BC330" "BC321" "BC266"
## [181] "BC243" "BC219" "BC216" "BC199" "BC192"
## [186] "BC167" "BC135" "BC131" "BC126" "BC125"
## [191] "BC108" "BC83" "BC80" "BC70" "BC586C"
## [196] "BC194C" "BC128C" "CC540" "CC531" "CC457"
## [201] "CC450" "CC447" "CC402" "CC392" "CC387"
## [206] "CC381" "CC378" "CC371" "CC359" "CC330"
## [211] "CC286" "CC283" "CC270" "CC262" "CC150"
## [216] "CC149" "CC138" "CC132" "CC130" "CC126"
## [221] "CC124" "CC114" "CC93" "CC61" "CC385C"
## [226] "CC338C" "CC171C" "AAT312" "AAT283" "LFY"
## [231] "AAT333" "AP3" "MgSTS17" "MgSTS18" "MgSTS21"
## [236] "MgSTS25" "MgSTS22" "MgSTS27" "MgSTS26" "MgSTS23"
## [241] "MgSTS28" "MgSTS105" "MgSTS120" "MgSTS93" "MgSTS133"
## [246] "MgSTS58" "MgSTS55" "MgSTS40" "MgSTS98" "MgSTS45"
## [251] "MgSTS11" "MgSTS132" "MgSTS212" "MgSTS228" "MgSTS229"
## [256] "MgSTS234" "MgSTS308" "MgSTS316" "MgSTS323" "MgSTS36"
## [261] "MgSTS43" "MgSTS437" "MgSTS48" "MgSTS49" "MgSTS59"
## [266] "MgSTS68" "MgSTS508" "MgSTS529" "MgSTS455" "MgSTS468"
## [271] "MgSTS480" "MgSTS474" "MgSTS113" "MgSTS106" "MgSTS69"
## [276] "MgSTS56" "MgSTS31" "MgSTS95" "MgSTS262" "MgSTS50"
## [281] "MgSTS76" "MgSTS388" "MgSTS330" "MgSTS332" "MgSTS326"
## [286] "MgSTS282B" "MgSTS282A" "MgSTS255" "MgSTS350" "MgSTS362"
## [291] "MgSTS344" "MgSTS37" "MgSTS34" "MgSTS426" "MgSTS453"
## [296] "MgSTS456" "MgSTS457" "MgSTS492" "MgSTS513" "MgSTS509"
## [301] "MgSTS500" "MgSTS430" "MgSTS381" "MgSTS314" "MgSTS251"
## [306] "MgSTS351" "MgSTS347" "MgSTS320" "MgSTS293" "MgSTS578"
## [311] "MgSTS571" "MgSTS574B" "MgSTS574a" "MgSTS579" "MgSTS638"
## [316] "MgSTS590" "MgSTS589" "MgSTS586" "MgSTS535" "MgSTS537"
## [321] "MgSTS538" "MgSTS536" "MgSTS539" "MgSTS563" "MgSTS558"
## [326] "MgSTS419" "MgSTS611" "MgSTS632" "MgSTS609" "MgSTS600"
## [331] "MgSTS565" "MgSTS606" "MgSTS577" "MgSTS438" "MgSTS477"
## [336] "MgSTS383" "MgSTS504A" "MgSTS504B" "MgSTS504C" "MgSTS545"
## [341] "MgSTS542A" "MgSTS542B" "MgSTS598" "MgSTS441" "MgSTS104"
## [346] "MgSTS511" "MgSTS621" "MgSTS622" "MgSTS459" "MgSTS220"
## [351] "MgSTS214" "MgSTS467" "MgSTS470" "MgSTS599" "MgSTS431"
## [356] "MgSTS440"ESTIMATING RECOMBINATION FRACTIONS
twopts_f2 <- rf_2pts(fake_f2_onemap, LOD = 6, max.rf = 0.37)## Computing 87153 recombination fractions:
##
## 0% ........................................... 100%suggest_lod(fake_f2_onemap) ## [1] 5.429707LOD suggest, but we used the LOD proposed by Fishman in original article
ASSIGNING MARKERS TO LINKAGE GROUPS
mark_all_f2 <- make_seq(twopts_f2, "all")FORMING THE GROUPS
LGs_f2 <- group(mark_all_f2)## Selecting markers:
## group 1
## ............................................................
## ......................
## group 2
## ......................
## group 3
## ............................................................
## ...........................
## group 4
## ........................................
## group 5
## .....................
## group 6
## ...................................................
## group 7
## ................................
## group 8
## ..........................
## group 9
## .............................
## group 10
## .....................LGs_f2## This is an object of class 'group'
## It was generated from the object "mark_all_f2"
##
## Criteria used to assign markers to groups:
## LOD = 6 , Maximum recombination fraction = 0.37
##
## No. markers: 418
## No. groups: 10
## No. linked markers: 411
## No. unlinked markers: 7
##
## Printing groups:
## Group 1 : 82 markers
## AA461 AA341 AA173C AA137 BA449 BA416 BA387 BA374 BA214 BA196 BA153 BA129 BB216 BB124 CA267 CA174 CA150 CA75 BD371 BD340 BD270 BD251 BD100 CA389C AAT225 AAT267 AAT265 BC542 BC374 BC80 BC526C BC194C CC447 CC320 CC138 CC93 CC61 CC53 AAT333 AP3 MgSTS17 MgSTS16 MgSTS18 MgSTS20 MgSTS19 MgSTS24 MgSTS26 MgSTS29 MgSTS38 MgSTS91 MgSTS93 MgSTS133 MgSTS98 CYCA aat356 MgSTS87 MgSTS212 MgSTS527 MgSTS520 MgSTS360 MgSTS341 MgSTS336 MgSTS350 MgSTS348 MgSTS358 MgSTS344 MgSTS471 MgSTS491 MgSTS500 MgSTS398 MgSTS380 MgSTS263 MgSTS578 MgSTS583 MgSTS631 MgSTS562 MgSTS561 MgSTS632 MgSTS494 MgSTS483 MgSTS598 MgSTS620
##
## Group 2 : 22 markers
## AA420 BA301 BA172 BA125 CA279 CA228 CB280 BD175 BD99 BC167 BC126 CC132 CC130 CC385C MgSTS316 MgSTS49 MgSTS106 MgSTS56 MgSTS457 MgSTS513 MgSTS589 MgSTS565
##
## Group 3 : 87 markers
## AA404 AA361 AA280 AA100 BA497 BA384 BA220 BA75 BB281 BB259 BB190 BB122 BB119 BB102 CA289 CA238 CA220 CA198 CA131 CA96 CB309 CB246 CB187 CB173 CB166 CB162 CB156 BD433 BD429 BD292 BD286 BD263 BD209 BD170 BD68 AA153C CA258C BB103C AAT261 AAT278 AAT374 AAT372 AG19 BC498 BC379 BC334 BC131 BC70 BC586C BC128C CC392 CC387 CC378 CC330 CC286 CC283 AAT312 AAT283 MgSTS27 MgSTS308 MgSTS43 MgSTS48 MgSTS70 MgSTS474 MgSTS95 MgSTS50 MgSTS75 MgSTS388 MgSTS332 MgSTS37 MgSTS34 MgSTS509 MgSTS251 MgSTS351 MgSTS293 MgSTS574B MgSTS574a MgSTS579 MgSTS535 MgSTS539 MgSTS609 MgSTS425 MgSTS435 MgSTS383 MgSTS441 MgSTS511 MgSTS214
##
## Group 4 : 40 markers
## AA384 AA166C AA66 BA210 BA113 BB208 CA497 CA415 CA399 CA384 CA297 CA233 CB329 CB257 BD411 BD243 BD239 BD130 BD115 AA346C AA374C BA279C CA183C AAT367 BC512 BC321 BC216 BC192 CC531 CC270 MgSTS132 MgSTS228 MgSTS234 MgSTS455 MgSTS262 MgSTS362 MgSTS492 MgSTS347 MgSTS477 MgSTS542B
##
## Group 5 : 21 markers
## AA378 AA268 AA163 BA69 BB210 BB186 CA264 CA226 CB230 BD316C BD173 AA118C AA454C BC506 CC342 CC124 MgSTS40 MgSTS245 MgSTS282A MgSTS255 MgSTS586
##
## Group 6 : 51 markers
## AA371C AA311 AA277 AA270 AA158 BA222 BA117 CA283 CA152C CB333 BD179 BD169 BD55 AAT230 AAT300 BC392 BC243 BC125 CC457 CC381 CC262 CC126 CC171C MgSTS21 MgSTS25 MgSTS22 MgSTS28 MgSTS105 MgSTS120 MgSTS58 MgSTS229 MgSTS323 MgSTS508 MgSTS529 MgSTS480 MgSTS426 MgSTS453 MgSTS456 MgSTS430 MgSTS314 MgSTS320 MgSTS606 MgSTS504A MgSTS504B MgSTS545 MgSTS542A MgSTS459 MgSTS220 MgSTS467 MgSTS431 MgSTS440
##
## Group 7 : 32 markers
## AA246 BA372 BA314 BA158 BB167 CA305 CA210 CA122 CB272 BD189C AAT217 AAT39 AAT211 AAT296 CYCB AAT242 CC450 CC359 CC338C MgSTS59 MgSTS69 MgSTS31 MgSTS76 MgSTS330 MgSTS381 MgSTS571 MgSTS590 MgSTS537 MgSTS538 MgSTS563 MgSTS504C MgSTS621
##
## Group 8 : 26 markers
## AA167 AA95 BA445 BA400 BA311 BB218 BB176 CA261 CA217 CA196 CA167 CB115 BA396C AAT222 BC108 BC83 CC540 CC402 LFY MgSTS468 MgSTS638 MgSTS536 MgSTS558 MgSTS611 MgSTS600 MgSTS470
##
## Group 9 : 29 markers
## BA394 BA175 BB182 CA378 CA140 CB216 BD242 BD143 AA296C BA245C AAT233 AAT272 AAT308 AAT364 BC546 BC478 BC388 BC376 BC330 BC266 BC219 CC149 CC114 MgSTS36 MgSTS437 MgSTS113 MgSTS282B MgSTS548 MgSTS438
##
## Group 10 : 21 markers
## BA334 BA145 BB198 CA315 CB172 CB126 CB55 CB263C AAT240 BC199 CC150 MgSTS55 MgSTS45 MgSTS11 MgSTS68 MgSTS326 MgSTS419 MgSTS577 MgSTS104 MgSTS622 MgSTS599
##
## Unlinked markers: 7 markers
## AA208 BB327 BB279 CA392 BC135 CC371 MgSTS23We can see that the markers were assigned to three linkage 10 groups and 7 with no unlinked markers (AA208 BB327 BB279 CA392 BC135 CC371 MgSTS23).
ORDERING MARKERS WITHIN LINKAGE GROUPS
The next step is to order the markers within each group, We can choose between Kosambi
set_map_fun(type = "kosambi")
LG2_f2 <- make_seq(LGs_f2, 2)
LG2_f2##
## Number of markers: 22
## Markers in the sequence:
## AA420 BA301 BA172 BA125 CA279 CA228 CB280 BD175 BD99 BC167 BC126 CC132
## CC130 CC385C MgSTS316 MgSTS49 MgSTS106 MgSTS56 MgSTS457 MgSTS513 MgSTS589
## MgSTS565
##
## Parameters not estimated.To order markers in this group, you can use a two-point based algorithm such as Recombination Counting and Ordering (Van Os et al., 2005)
LG2_rcd_f2 <- rcd(LG2_f2)##
## order obtained using RCD algorithm:
##
## 50 252 2 245 90 296 38 209 345 302 315 109 45 140 317 369 348 388 244 212 148 84
##
## calculating multipoint map using tol = 1e-04 .LG2_f2_ord <- order_seq(input.seq = LG2_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 50 252 2 245 90 296 38 209 345 302 315 109 45 140 317 369 348 388 244 212 148 84
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 388 --> MgSTS565 : ......
## 315 --> MgSTS106 : ......
## 317 --> MgSTS56 : ......
## 369 --> MgSTS589 : .......
## 252 --> CC385C : ........
## 302 --> MgSTS49 : ........
## 345 --> MgSTS457 : .........
## 90 --> CA228 : ..........
## 38 --> BA301 : ..........
## 45 --> BA172 : ...........
## 209 --> BC167 : ...........
## 212 --> BC126 : ............
## 2 --> AA420 : .............
## 140 --> BD175 : ..............
## 148 --> BD99 : ...............
## 244 --> CC132 : ...............
## 245 --> CC130 : ...............
##
## LOD threshold = 3
##
## Positioned markers: 50 2 245 296 38 209 109 302 345 140 317 369 348 212 84
##
## Markers not placed on the map: 45 90 148 244 252 315 388
##
##
## Calculating LOD-Scores
## 45 --> BA172 : ................
## 90 --> CA228 : ................
## 148 --> BD99 : ................
## 244 --> CC132 : ................
## 252 --> CC385C : ................
## 315 --> MgSTS106 : ................
## 388 --> MgSTS565 : ................
##
##
## Placing remaining marker(s) at most likely position
## 388 --> MgSTS565 : ................
## 315 --> MgSTS106 : .................
## 252 --> CC385C : ..................
## 244 --> CC132 : ...................
## 45 --> BA172 : ....................
## 90 --> CA228 : .....................
## 148 --> BD99 : ......................
##
## Estimating final genetic map using tol = 10E-5.LG2_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 50 BA125 0.00
## 2 AA420 10.10
## 245 CC130 19.51
## 296 MgSTS316 27.58
## 38 BA301 59.11
## 209 BC167 68.81
## 109 CB280 77.33
## 302 MgSTS49 82.92
## 345 MgSTS457 87.85
## 140 BD175 92.15
## 317 MgSTS56 96.90
## 369 MgSTS589 97.70
## 348 MgSTS513 109.97
## 212 BC126 121.08
## 84 CA279 150.67
##
## 15 markers log-likelihood: -1670.228
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------
## | | 45 | 90 | 148 | 244 | 252 | 315 | 388 |
## |-----|-----|-----|-----|-----|-----|-----|-----|
## | | | | | | *** | | |
## | 50 | | | | | | | |
## | | | | | | ** | | |
## | 2 | | | | | | | |
## | | | ** | | | | | |
## | 245 | | | | | | | |
## | | | *** | | | | | |
## | 296 | | | | | | | |
## | | | | | | | | |
## | 38 | | | | | | | |
## | | | | | | | | |
## | 209 | | | | | | | |
## | | *** | | | | | | |
## | 109 | | | | | | | |
## | | ** | | | | | | |
## | 302 | | | | | | | |
## | | | | | | | *** | |
## | 345 | | | | | | | |
## | | | | | | | | |
## | 140 | | | | | | | |
## | | | | | | | | |
## | 317 | | | | | | | |
## | | | | | | | | |
## | 369 | | | | | | | |
## | | | | | *** | | | *** |
## | 348 | | | | | | | |
## | | | | *** | ** | | | |
## | 212 | | | | | | | |
## | | | | ** | ** | | | |
## | 84 | | | | | | | |
## | | | | | | | | |
## -------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)Check the order obtained. Note that markers 45, 90, 148, 244, 252, 315, 388 could not be safely mapped to a single position where ndicates the most likely position
(Ligação_grupo_2 <- make_seq(LG2_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 252 CC385C 0.00
## 50 BA125 13.96
## 2 AA420 21.28
## 245 CC130 31.80
## 90 CA228 33.43
## 296 MgSTS316 40.51
## 38 BA301 71.28
## 209 BC167 81.30
## 45 BA172 88.99
## 109 CB280 90.82
## 302 MgSTS49 96.17
## 315 MgSTS106 97.07
## 345 MgSTS457 101.69
## 140 BD175 106.01
## 317 MgSTS56 110.66
## 369 MgSTS589 111.43
## 244 CC132 120.76
## 388 MgSTS565 126.91
## 348 MgSTS513 128.34
## 148 BD99 137.89
## 212 BC126 138.50
## 84 CA279 167.72
##
## 22 markers log-likelihood: -2142.921ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)## 252-50-2-245-90-|-296-...
## Alternative orders:
## 252 50 2 245 90 ... : 0.00
## 252 50 2 90 245 ... : -0.10
## 50 252 2 245 90 ... : -3.48
## 50 252 2 90 245 ... : -3.57
## 252 2 50 90 245 ... : -5.17
## 252 2 50 245 90 ... : -5.76
##
## ...-252-|-50-2-245-90-296-|-38-...
## Alternative orders:
## 50 2 245 90 296 ... : 0.00
## 50 2 90 245 296 ... : -0.10
## 50 2 245 296 90 ... : -3.65
## 2 50 90 245 296 ... : -5.17
## 2 50 245 90 296 ... : -5.76
##
## ...-50-|-2-245-90-296-38-|-209-...
## Alternative orders:
## ... 2 245 90 296 38 ... : 0.00
## ... 2 90 245 296 38 ... : -0.10
## ... 2 245 296 90 38 ... : -3.65
##
## ...-2-|-245-90-296-38-209-|-45-...
## Alternative orders:
## ... 245 90 296 38 209 ... : 0.00
## ... 90 245 296 38 209 ... : -0.10
## ... 245 296 90 38 209 ... : -3.65
##
## ...-245-|-90-296-38-209-45-|-109-...
## Alternative orders:
## ... 90 296 38 209 45 ... : 0.00
## ... 296 90 38 209 45 ... : -3.65
##
## ...-90-|-296-38-209-45-109-|-302-...
## Alternative orders:
## ... 296 38 209 45 109 ... : 0.00
## ... 296 38 209 109 45 ... : -0.54
##
## ...-296-|-38-209-45-109-302-|-315-...
## Alternative orders:
## ... 38 209 45 109 302 ... : 0.00
## ... 38 209 109 45 302 ... : -0.54
##
## ...-38-|-209-45-109-302-315-|-345-...
## Alternative orders:
## ... 209 45 109 302 315 ... : 0.00
## ... 209 109 45 302 315 ... : -0.54
## ... 209 45 109 315 302 ... : -3.34
## ... 209 109 45 315 302 ... : -3.89
## ... 209 45 302 315 109 ... : -4.23
##
## ...-209-|-45-109-302-315-345-|-140-...
## Alternative orders:
## ... 45 109 302 315 345 ... : 0.00
## ... 109 45 302 315 345 ... : -0.54
## ... 45 109 315 302 345 ... : -3.34
## ... 109 45 315 302 345 ... : -3.89
## ... 45 302 315 109 345 ... : -4.23
##
## ...-45-|-109-302-315-345-140-|-317-...
## Alternative orders:
## ... 109 302 315 345 140 ... : 0.00
## ... 109 315 302 345 140 ... : -3.34
## ... 302 315 109 345 140 ... : -4.23
##
## ...-109-|-302-315-345-140-317-|-369-...
## Alternative orders:
## ... 302 315 345 140 317 ... : 0.00
## ... 315 302 345 140 317 ... : -3.34
##
## ...-302-|-315-345-140-317-369-|-244-...
## Alternative orders:
## ... 315 345 140 317 369 ... : 0.00
## ... 315 345 140 369 317 ... : -1.83
## ... 315 345 369 317 140 ... : -4.46
## ... 315 345 317 369 140 ... : -5.29
##
## ...-315-|-345-140-317-369-244-|-388-...
## Alternative orders:
## ... 345 140 317 369 244 ... : 0.00
## ... 345 140 369 317 244 ... : -1.83
## ... 345 369 317 140 244 ... : -4.46
## ... 345 317 369 140 244 ... : -5.29
##
## ...-345-|-140-317-369-244-388-|-348-...
## Alternative orders:
## ... 140 317 369 244 388 ... : 0.00
## ... 140 369 317 244 388 ... : -1.83
## ... 369 317 140 244 388 ... : -4.46
## ... 317 369 140 244 388 ... : -5.29
##
## ...-140-|-317-369-244-388-348-|-148-...
## Alternative orders:
## ... 317 369 388 348 244 ... : 0.00
## ... 317 369 348 388 244 ... : -1.15
## ... 317 369 244 388 348 ... : -1.28
## ... 369 317 388 348 244 ... : -1.90
## ... 369 317 348 388 244 ... : -3.04
## ... 369 317 244 388 348 ... : -3.11
## ... 317 369 244 348 388 ... : -4.29
##
## ...-317-|-369-244-388-348-148-|-212-...
## Alternative orders:
## ... 369 388 348 244 148 ... : 0.00
## ... 369 348 388 244 148 ... : -1.15
## ... 369 244 388 348 148 ... : -1.28
## ... 369 244 148 388 348 ... : -3.45
## ... 369 244 348 388 148 ... : -4.29
## ... 369 388 348 148 244 ... : -4.62
## ... 369 348 388 148 244 ... : -5.72
##
## ...-369-|-244-388-348-148-212-|-84-...
## Alternative orders:
## ... 388 348 244 148 212 : 0.00
## ... 388 348 212 244 148 : -0.25
## ... 348 388 244 148 212 : -1.15
## ... 244 388 348 148 212 : -1.28
## ... 244 388 348 212 148 : -1.33
## ... 388 348 244 212 148 : -1.79
## ... 348 388 212 244 148 : -2.35
## ... 244 148 388 348 212 : -3.45
## ... 348 388 244 212 148 : -3.63
## ... 388 348 212 148 244 : -4.25
## ... 244 348 388 148 212 : -4.29
## ... 244 348 388 212 148 : -4.38
## ... 388 348 148 244 212 : -4.62
## ... 348 388 148 244 212 : -5.72
##
## 244-|-388-348-148-212-84
## Alternative orders:
## 388 348 148 212 84 ... : 0.00
## 388 348 212 148 84 ... : -0.04
## 148 388 348 212 84 ... : -2.17
## 348 388 148 212 84 ... : -3.01
## 348 388 212 148 84 ... : -3.10The second argument, ws = 5, means that subsets (windows) of five markers will be permutated sequentially (5! orders for each window), to search for other plausible orders.
However, the best order was that obtained with the order_seq function
HGL2<-rf_graph_table(Ligação_grupo_2, axis.cex=.6, inter=FALSE)
Removing markers, by ripple algoritm results, this markets 244, 148 is not correct position. Removing markers, by graphical resuts too.
Running again
(LG2seq_f2_rm <- drop_marker(Ligação_grupo_2, c(244, 148)))##
## Number of markers: 20
## Markers in the sequence:
## CC385C BA125 AA420 CC130 CA228 MgSTS316 BA301 BC167 BA172 CB280 MgSTS49
## MgSTS106 MgSTS457 BD175 MgSTS56 MgSTS589 MgSTS565 MgSTS513 BC126 CA279
##
## Parameters not estimated.LG2_rcd_f2_rm <- rcd(LG2seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 50 252 2 245 90 296 38 209 345 302 315 109 45 140 317 369 348 388 212 84
##
## calculating multipoint map using tol = 1e-04 .LG2_f2_ord_rm <- order_seq(input.seq = LG2_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 50 252 2 245 90 296 38 209 345 302 315 109 45 140 317 369 348 388 212 84
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
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##
##
##
## Running try algorithm
## 388 --> MgSTS565 : ......
## 315 --> MgSTS106 : .......
## 369 --> MgSTS589 : .......
## 252 --> CC385C : .......
## 348 --> MgSTS513 : .......
## 345 --> MgSTS457 : .......
## 90 --> CA228 : ........
## 38 --> BA301 : ........
## 45 --> BA172 : .........
## 209 --> BC167 : ..........
## 212 --> BC126 : ...........
## 109 --> CB280 : ............
## 2 --> AA420 : ............
## 140 --> BD175 : .............
## 245 --> CC130 : ..............
##
## LOD threshold = 3
##
## Positioned markers: 50 2 245 296 38 209 45 302 345 140 317 388 212 84
##
## Markers not placed on the map: 252 90 315 109 369 348
##
##
## Calculating LOD-Scores
## 252 --> CC385C : ...............
## 90 --> CA228 : ...............
## 315 --> MgSTS106 : ...............
## 109 --> CB280 : ...............
## 369 --> MgSTS589 : ...............
## 348 --> MgSTS513 : ...............
##
##
## Placing remaining marker(s) at most likely position
## 315 --> MgSTS106 : ...............
## 348 --> MgSTS513 : ................
## 369 --> MgSTS589 : .................
## 252 --> CC385C : ..................
## 109 --> CB280 : ...................
## 90 --> CA228 : ....................
##
## Estimating final genetic map using tol = 10E-5.LG2_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 50 BA125 0.00
## 2 AA420 10.05
## 245 CC130 19.44
## 296 MgSTS316 27.55
## 38 BA301 59.95
## 209 BC167 70.07
## 45 BA172 77.61
## 302 MgSTS49 84.51
## 345 MgSTS457 89.63
## 140 BD175 93.83
## 317 MgSTS56 97.94
## 388 MgSTS565 110.27
## 212 BC126 121.78
## 84 CA279 151.30
##
## 14 markers log-likelihood: -1645.958
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------
## | | 252 | 90 | 315 | 109 | 369 | 348 |
## |-----|-----|-----|-----|-----|-----|-----|
## | | *** | | | | | |
## | 50 | | | | | | |
## | | ** | | | | | |
## | 2 | | | | | | |
## | | | ** | | | | |
## | 245 | | | | | | |
## | | | *** | | | | |
## | 296 | | | | | | |
## | | | | | | | |
## | 38 | | | | | | |
## | | | | | | | |
## | 209 | | | | | | |
## | | | | | ** | | |
## | 45 | | | | | | |
## | | | | | *** | | |
## | 302 | | | | | | |
## | | | | *** | | | |
## | 345 | | | | | | |
## | | | | | | | |
## | 140 | | | | | | |
## | | | | | | * | |
## | 317 | | | | | | |
## | | | | | | *** | |
## | 388 | | | | | | |
## | | | | | | | *** |
## | 212 | | | | | | |
## | | | | | | | |
## | 84 | | | | | | |
## | | | | | | | |
## -------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_2rm <- make_seq(LG2_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 252 CC385C 0.00
## 50 BA125 13.96
## 2 AA420 21.28
## 245 CC130 31.80
## 90 CA228 33.44
## 296 MgSTS316 40.51
## 38 BA301 71.28
## 209 BC167 81.30
## 45 BA172 88.99
## 109 CB280 90.82
## 302 MgSTS49 96.17
## 315 MgSTS106 97.07
## 345 MgSTS457 101.68
## 140 BD175 106.01
## 317 MgSTS56 110.68
## 369 MgSTS589 111.42
## 388 MgSTS565 123.86
## 348 MgSTS513 125.33
## 212 BC126 135.56
## 84 CA279 164.80
##
## 20 markers log-likelihood: -2034.836P1_HGL2 <- rf_graph_table(Ligação_grupo_2rm, axis.cex=.6, inter=FALSE)
The best order was that obtained WITH THE FIRST HEAT MAP. The final estimated map can then be printed using the next group, without removed markets. After, assign a linking group according to the data of the article, reference (Fishman et al., 2001)
Ligação_grupo_2##
## Printing map:
##
## Markers Position
##
## 252 CC385C 0.00
## 50 BA125 13.96
## 2 AA420 21.28
## 245 CC130 31.80
## 90 CA228 33.43
## 296 MgSTS316 40.51
## 38 BA301 71.28
## 209 BC167 81.30
## 45 BA172 88.99
## 109 CB280 90.82
## 302 MgSTS49 96.17
## 315 MgSTS106 97.07
## 345 MgSTS457 101.69
## 140 BD175 106.01
## 317 MgSTS56 110.66
## 369 MgSTS589 111.43
## 244 CC132 120.76
## 388 MgSTS565 126.91
## 348 MgSTS513 128.34
## 148 BD99 137.89
## 212 BC126 138.50
## 84 CA279 167.72
##
## 22 markers log-likelihood: -2142.921GL2<-Ligação_grupo_2ORDERING MARKERS THE NEXT LINKAGE GROUP
the next step is to order the markers within group 4, We can do the same steps with the previou group.
set_map_fun(type = "kosambi")
LG4_f2 <- make_seq(LGs_f2, 4)
LG4_f2##
## Number of markers: 40
## Markers in the sequence:
## AA384 AA166C AA66 BA210 BA113 BB208 CA497 CA415 CA399 CA384 CA297 CA233
## CB329 CB257 BD411 BD243 BD239 BD130 BD115 AA346C AA374C BA279C CA183C
## AAT367 BC512 BC321 BC216 BC192 CC531 CC270 MgSTS132 MgSTS228 MgSTS234
## MgSTS455 MgSTS262 MgSTS362 MgSTS492 MgSTS347 MgSTS477 MgSTS542B
##
## Parameters not estimated.LG4_rcd_f2 <- rcd(LG4_f2)##
## order obtained using RCD algorithm:
##
## 126 4 178 239 111 293 310 202 77 223 208 81 206 62 145 155 52 159 291 347 336 395 18 161 24 73 156 89 75 42 289 358 191 107 403 74 135 321 137 146
##
## calculating multipoint map using tol = 1e-04 .LG4_f2_ord <- order_seq(input.seq = LG4_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 126 4 178 239 111 293 310 202 77 223 208 81 206 62 145 155 52 159 291 347 336 395 18 161 24 73 156 89 75 42 289 358 191 107 403 74 135 321 137 146
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 161 --> CA183C : ......
## 156 --> AA374C : ......
## 395 --> MgSTS477 : ......
## 18 --> AA166C : .......
## 155 --> AA346C : ........
## 159 --> BA279C : .........
## 358 --> MgSTS347 : ..........
## 291 --> MgSTS228 : ..........
## 403 --> MgSTS542B : ...........
## 289 --> MgSTS132 : ...........
## 336 --> MgSTS362 : ...........
## 293 --> MgSTS234 : ............
## 310 --> MgSTS455 : ............
## 178 --> AAT367 : ............
## 321 --> MgSTS262 : ............
## 111 --> CB257 : .............
## 89 --> CA233 : .............
## 75 --> CA399 : .............
## 4 --> AA384 : .............
## 145 --> BD130 : .............
## 137 --> BD239 : ..............
## 206 --> BC216 : ..............
## 191 --> BC512 : ..............
## 239 --> CC270 : ..............
## 62 --> BB208 : ..............
## 107 --> CB329 : ...............
## 77 --> CA384 : ...............
## 81 --> CA297 : ................
## 73 --> CA497 : ................
## 74 --> CA415 : ................
## 24 --> AA66 : ................
## 52 --> BA113 : .................
## 135 --> BD243 : ..................
## 202 --> BC321 : ...................
## 223 --> CC531 : ...................
##
## LOD threshold = 3
##
## Positioned markers: 42 126 77 135 24 18 395 336 321 347 208 291 62 52 155 145 159 146
##
## Markers not placed on the map: 4 178 239 111 293 310 202 223 81 206 161 73 156 89 75 289 358 191 107 403 74 137
##
##
## Calculating LOD-Scores
## 4 --> AA384 : ...................
## 178 --> AAT367 : ...................
## 239 --> CC270 : ...................
## 111 --> CB257 : ...................
## 293 --> MgSTS234 : ...................
## 310 --> MgSTS455 : ...................
## 202 --> BC321 : ...................
## 223 --> CC531 : ...................
## 81 --> CA297 : ...................
## 206 --> BC216 : ...................
## 161 --> CA183C : ...................
## 73 --> CA497 : ...................
## 156 --> AA374C : ...................
## 89 --> CA233 : ...................
## 75 --> CA399 : ...................
## 289 --> MgSTS132 : ...................
## 358 --> MgSTS347 : ...................
## 191 --> BC512 : ...................
## 107 --> CB329 : ...................
## 403 --> MgSTS542B : ...................
## 74 --> CA415 : ...................
## 137 --> BD239 : ...................
##
##
## Placing remaining marker(s) at most likely position
## 137 --> BD239 : ...................
## 206 --> BC216 : ....................
## 293 --> MgSTS234 : .....................
## 156 --> AA374C : ......................
## 111 --> CB257 : .......................
## 223 --> CC531 : ........................
## 239 --> CC270 : .........................
## 202 --> BC321 : ..........................
## 73 --> CA497 : ...........................
## 178 --> AAT367 : ............................
## 4 --> AA384 : .............................
## 310 --> MgSTS455 : ..............................
## 161 --> CA183C : ...............................
## 74 --> CA415 : ................................
## 81 --> CA297 : .................................
## 289 --> MgSTS132 : ..................................
## 191 --> BC512 : ...................................
## 107 --> CB329 : ....................................
## 403 --> MgSTS542B : .....................................
## 358 --> MgSTS347 : ......................................
## 89 --> CA233 : .......................................
## 75 --> CA399 : ........................................
##
## Estimating final genetic map using tol = 10E-5.LG4_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 42 BA210 0.00
## 126 BD411 77.72
## 77 CA384 108.06
## 135 BD243 147.17
## 24 AA66 158.51
## 18 AA166C 170.83
## 395 MgSTS477 178.72
## 336 MgSTS362 184.32
## 321 MgSTS262 193.79
## 347 MgSTS492 203.61
## 208 BC192 213.34
## 291 MgSTS228 224.80
## 62 BB208 226.93
## 52 BA113 232.71
## 155 AA346C 235.90
## 145 BD130 241.12
## 159 BA279C 249.02
## 146 BD115 265.96
##
## 18 markers log-likelihood: -2234.91
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------------------------------------------------------------
## | | 4 | 178 | 239 | 111 | 293 | 310 | 202 | 223 | 81 | 206 | 161 | 73 | 156 | 89 | 75 | 289 | 358 | 191 | 107 | 403 | 74 | 137 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | ** | ** | * | * | | | | | | | | | | ** | *** | ** | ** | ** | ** | ** | ** | |
## | 42 | | | | | | | | | | | | | | | | | | | | | | |
## | | *** | *** | *** | *** | *** | | | | | | | | | ** | ** | *** | *** | *** | *** | *** | *** | |
## | 126 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | * | * | | | | | | | | | | | | | | |
## | 77 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | *** | | | | * | *** | *** | | | | | | | | |
## | 135 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | ** | *** | * | | | | | | | | | |
## | 24 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | *** | | | | | | | | | | | |
## | 18 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | |
## | 395 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | |
## | 336 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | |
## | 321 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | |
## | 347 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | ** | | | | | | | | | | | | | |
## | 208 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | ** | | | *** | | | | | | | | | | | | | |
## | 291 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | |
## | 62 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | *** | | | | | | | | | | | | | | | | |
## | 52 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | |
## | 155 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | |
## | 145 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | * | | | | | | | | | | | | | | | *** |
## | 159 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | * | | | | *** | | | | | | | | | | | | |
## | 146 | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | * | *** | | | | | | | | | | | | | | | |
## -------------------------------------------------------------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_4 <- make_seq(LG4_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 74 CA415 0.00
## 191 BC512 14.15
## 358 MgSTS347 18.60
## 289 MgSTS132 23.76
## 42 BA210 30.75
## 75 CA399 31.02
## 107 CB329 41.64
## 403 MgSTS542B 45.50
## 4 AA384 448.46
## 178 AAT367 474.18
## 293 MgSTS234 500.25
## 111 CB257 507.20
## 239 CC270 516.28
## 202 BC321 531.17
## 310 MgSTS455 541.14
## 126 BD411 569.02
## 77 CA384 598.44
## 223 CC531 617.32
## 89 CA233 653.65
## 156 AA374C 661.76
## 73 CA497 666.24
## 135 BD243 673.00
## 161 CA183C 682.10
## 24 AA66 687.39
## 18 AA166C 696.16
## 395 MgSTS477 704.01
## 336 MgSTS362 709.58
## 321 MgSTS262 719.01
## 347 MgSTS492 728.86
## 208 BC192 739.03
## 81 CA297 743.03
## 291 MgSTS228 750.66
## 62 BB208 752.37
## 52 BA113 758.30
## 155 AA346C 761.51
## 145 BD130 766.41
## 137 BD239 772.85
## 159 BA279C 781.83
## 206 BC216 795.61
## 146 BD115 816.95
##
## 40 markers log-likelihood: -4757.213#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_4, axis.cex=.6, inter=FALSE)
LG4seq_f2_rm <- drop_marker(Ligação_grupo_4, c(89,156,223,137,146))
LG4_rcd_f2_rm <- rcd(LG4seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 74 403 107 191 358 289 75 42 135 73 24 161 18 395 336 347 291 159 52 155 145 62 208 81 206 202 310 293 111 239 178 4 126 77 321
##
## calculating multipoint map using tol = 1e-04 .LG4_f2_ord_rm <- order_seq(input.seq = LG4_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 74 403 107 191 358 289 75 42 135 73 24 161 18 395 336 347 291 159 52 155 145 62 208 81 206 202 310 293 111 239 178 4 126 77 321
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 161 --> CA183C : ......
## 18 --> AA166C : .......
## 395 --> MgSTS477 : ........
## 155 --> AA346C : .........
## 358 --> MgSTS347 : ..........
## 291 --> MgSTS228 : ...........
## 403 --> MgSTS542B : ............
## 289 --> MgSTS132 : ............
## 336 --> MgSTS362 : .............
## 310 --> MgSTS455 : ..............
## 293 --> MgSTS234 : ..............
## 178 --> AAT367 : ...............
## 347 --> MgSTS492 : ................
## 111 --> CB257 : .................
## 75 --> CA399 : .................
## 4 --> AA384 : ..................
## 145 --> BD130 : ..................
## 191 --> BC512 : ..................
## 208 --> BC192 : ...................
## 206 --> BC216 : ...................
## 239 --> CC270 : ...................
## 62 --> BB208 : ....................
## 107 --> CB329 : .....................
## 81 --> CA297 : .....................
## 77 --> CA384 : ......................
## 24 --> AA66 : .......................
## 42 --> BA210 : .......................
## 52 --> BA113 : .......................
## 135 --> BD243 : .......................
## 126 --> BD411 : ........................
##
## LOD threshold = 3
##
## Positioned markers: 191 358 289 75 74 73 135 161 18 395 336 321 347 291 62 81 159 155 77 126 202 239 293 178
##
## Markers not placed on the map: 403 107 42 24 52 145 208 206 310 111 4
##
##
## Calculating LOD-Scores
## 403 --> MgSTS542B : .........................
## 107 --> CB329 : .........................
## 42 --> BA210 : .........................
## 24 --> AA66 : .........................
## 52 --> BA113 : .........................
## 145 --> BD130 : .........................
## 208 --> BC192 : .........................
## 206 --> BC216 : .........................
## 310 --> MgSTS455 : .........................
## 111 --> CB257 : .........................
## 4 --> AA384 : .........................
##
##
## Placing remaining marker(s) at most likely position
## 208 --> BC192 : .........................
## 4 --> AA384 : ..........................
## 111 --> CB257 : ...........................
## 145 --> BD130 : ............................
## 52 --> BA113 : .............................
## 403 --> MgSTS542B : ..............................
## 310 --> MgSTS455 : ...............................
## 206 --> BC216 : ................................
## 107 --> CB329 : .................................
## 24 --> AA66 : ..................................
## 42 --> BA210 : ...................................
##
## Estimating final genetic map using tol = 10E-5.LG4_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 191 BC512 0.00
## 358 MgSTS347 4.49
## 289 MgSTS132 9.71
## 75 CA399 16.96
## 74 CA415 23.24
## 73 CA497 42.39
## 135 BD243 49.61
## 161 CA183C 60.02
## 18 AA166C 70.39
## 395 MgSTS477 78.26
## 336 MgSTS362 83.84
## 321 MgSTS262 93.32
## 347 MgSTS492 103.25
## 291 MgSTS228 112.14
## 62 BB208 114.56
## 81 CA297 117.14
## 159 BA279C 124.02
## 155 AA346C 134.28
## 77 CA384 152.66
## 126 BD411 182.30
## 202 BC321 206.05
## 239 CC270 220.71
## 293 MgSTS234 231.12
## 178 AAT367 257.61
##
## 24 markers log-likelihood: -3055.622
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------
## | | 403 | 107 | 42 | 24 | 52 | 145 | 208 | 206 | 310 | 111 | 4 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | *** | *** | | | | | | | | | |
## | 191 | | | | | | | | | | | |
## | | * | ** | | | | | | | | | |
## | 358 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 289 | | | | | | | | | | | |
## | | | | *** | | | | | | | | |
## | 75 | | | | | | | | | | | |
## | | | | ** | | | | | | | | |
## | 74 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 73 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 135 | | | | | | | | | | | |
## | | | | | *** | | | | | | | |
## | 161 | | | | | | | | | | | |
## | | | | | ** | | | | | | | |
## | 18 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 395 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 336 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 321 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 347 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 291 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 62 | | | | | | | | | | | |
## | | | | | | | | | ** | | | |
## | 81 | | | | | | | | | | | |
## | | | | | | | | | *** | | | |
## | 159 | | | | | | | | | | | |
## | | | | | | *** | *** | | | | | |
## | 155 | | | | | | | | | | | |
## | | | | | | * | * | *** | ** | | | |
## | 77 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 126 | | | | | | | | | | | |
## | | | | | | | | | | *** | | |
## | 202 | | | | | | | | | | | |
## | | | | | | | | | | ** | | |
## | 239 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 293 | | | | | | | | | | | |
## | | | | | | | | | | | *** | |
## | 178 | | | | | | | | | | | |
## | | | | | | | | | | | | *** |
## -------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_4rm <- make_seq(LG4_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 107 CB329 0.00
## 403 MgSTS542B 4.18
## 191 BC512 10.40
## 358 MgSTS347 14.49
## 289 MgSTS132 19.99
## 42 BA210 26.99
## 75 CA399 27.65
## 74 CA415 40.30
## 73 CA497 59.03
## 135 BD243 66.20
## 24 AA66 75.96
## 161 CA183C 82.58
## 18 AA166C 92.96
## 395 MgSTS477 100.81
## 336 MgSTS362 106.39
## 321 MgSTS262 115.87
## 347 MgSTS492 125.79
## 291 MgSTS228 134.70
## 62 BB208 137.12
## 81 CA297 139.71
## 159 BA279C 146.52
## 145 BD130 154.97
## 52 BA113 156.86
## 155 AA346C 160.49
## 208 BC192 172.96
## 206 BC216 187.69
## 77 CA384 204.38
## 126 BD411 232.55
## 310 MgSTS455 258.47
## 202 BC321 268.31
## 239 CC270 283.89
## 293 MgSTS234 293.64
## 111 CB257 301.73
## 178 AAT367 323.34
## 4 AA384 349.12
##
## 35 markers log-likelihood: -4096.503HGL4<- rf_graph_table(Ligação_grupo_4rm, axis.cex=.6, inter=FALSE)
GL4 <- Ligação_grupo_4rmORDERING MARKERS THE NEXT LINKAGE GROUP
The next step is to order the markers within group 5, We can do the same steps with the previou group
set_map_fun(type = "kosambi")
LG5_f2 <- make_seq(LGs_f2, 5)
LG5_f2##
## Number of markers: 21
## Markers in the sequence:
## AA378 AA268 AA163 BA69 BB210 BB186 CA264 CA226 CB230 BD316C BD173 AA118C
## AA454C BC506 CC342 CC124 MgSTS40 MgSTS245 MgSTS282A MgSTS255 MgSTS586
##
## Parameters not estimated.LG5_rcd_f2 <- rcd(LG5_f2)##
## order obtained using RCD algorithm:
##
## 65 247 282 5 371 54 141 113 86 91 129 61 294 13 157 234 19 192 332 333 152
##
## calculating multipoint map using tol = 1e-04 .LG5_f2_ord <- order_seq(input.seq = LG5_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 65 247 282 5 371 54 141 113 86 91 129 61 294 13 157 234 19 192 332 333 152
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 157 --> AA454C : ......
## 282 --> MgSTS40 : ......
## 371 --> MgSTS586 : .......
## 294 --> MgSTS245 : ........
## 333 --> MgSTS255 : .........
## 332 --> MgSTS282A : ..........
## 86 --> CA264 : ...........
## 5 --> AA378 : ............
## 19 --> AA163 : .............
## 141 --> BD173 : ..............
## 192 --> BC506 : ...............
## 61 --> BB210 : ................
## 113 --> CB230 : ................
## 91 --> CA226 : .................
## 13 --> AA268 : .................
## 247 --> CC124 : ..................
##
## LOD threshold = 3
##
## Positioned markers: 65 247 282 371 54 113 129 5 141 86 294 13 234 19 192 332 333 152
##
## Markers not placed on the map: 91 61 157
##
##
## Calculating LOD-Scores
## 91 --> CA226 : ...................
## 61 --> BB210 : ...................
## 157 --> AA454C : ...................
##
##
## Placing remaining marker(s) at most likely position
## 157 --> AA454C : ...................
## 61 --> BB210 : ....................
## 91 --> CA226 : .....................
##
## Estimating final genetic map using tol = 10E-5.LG5_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 65 BB186 0.00
## 247 CC124 6.76
## 282 MgSTS40 16.85
## 371 MgSTS586 38.50
## 54 BA69 41.86
## 113 CB230 46.65
## 129 BD316C 48.49
## 5 AA378 56.22
## 141 BD173 62.93
## 86 CA264 67.87
## 294 MgSTS245 79.18
## 13 AA268 87.75
## 234 CC342 97.44
## 19 AA163 110.53
## 192 BC506 127.43
## 332 MgSTS282A 147.83
## 333 MgSTS255 151.88
## 152 AA118C 179.97
##
## 18 markers log-likelihood: -2214.558
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------
## | | 91 | 61 | 157 |
## |-----|-----|-----|-----|
## | | | | |
## | 65 | | | |
## | | | | |
## | 247 | | | |
## | | | | |
## | 282 | | | |
## | | | | |
## | 371 | | | |
## | | | | |
## | 54 | | | |
## | | | | |
## | 113 | | | |
## | | | *** | |
## | 129 | | | |
## | | ** | | |
## | 5 | | | |
## | | *** | | |
## | 141 | | | |
## | | * | | |
## | 86 | | | |
## | | * | | |
## | 294 | | | |
## | | | | |
## | 13 | | | |
## | | | | |
## | 234 | | | |
## | | | | *** |
## | 19 | | | |
## | | | | |
## | 192 | | | |
## | | | | |
## | 332 | | | |
## | | | | |
## | 333 | | | |
## | | | | |
## | 152 | | | |
## | | | | |
## -------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_5 <- make_seq(LG5_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 65 BB186 0.00
## 247 CC124 6.78
## 282 MgSTS40 16.83
## 371 MgSTS586 38.39
## 54 BA69 41.62
## 113 CB230 46.20
## 61 BB210 47.75
## 129 BD316C 49.47
## 5 AA378 56.86
## 91 CA226 60.30
## 141 BD173 63.72
## 86 CA264 68.83
## 294 MgSTS245 80.74
## 13 AA268 90.11
## 234 CC342 97.67
## 157 AA454C 105.03
## 19 AA163 114.35
## 192 BC506 130.54
## 332 MgSTS282A 149.72
## 333 MgSTS255 153.77
## 152 AA118C 181.81
##
## 21 markers log-likelihood: -2416.743#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_5, axis.cex=.6, inter=FALSE)
LG5seq_f2_rm <- drop_marker(Ligação_grupo_5, c(91,54))
LG5_rcd_f2_rm <- rcd(LG5seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 65 247 282 61 129 371 5 141 113 86 294 13 157 234 19 192 332 333 152
##
## calculating multipoint map using tol = 1e-04 .LG5_f2_ord_rm <- order_seq(input.seq = LG5_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 65 247 282 61 129 371 5 141 113 86 294 13 157 234 19 192 332 333 152
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 157 --> AA454C : ......
## 282 --> MgSTS40 : .......
## 129 --> BD316C : ........
## 294 --> MgSTS245 : .........
## 333 --> MgSTS255 : ..........
## 332 --> MgSTS282A : ...........
## 5 --> AA378 : ............
## 19 --> AA163 : .............
## 141 --> BD173 : ..............
## 192 --> BC506 : ...............
## 61 --> BB210 : ................
## 113 --> CB230 : ................
## 13 --> AA268 : .................
## 247 --> CC124 : .................
##
## LOD threshold = 3
##
## Positioned markers: 65 247 282 371 113 129 5 141 86 294 234 157 19 192 332 333 152
##
## Markers not placed on the map: 61 13
##
##
## Calculating LOD-Scores
## 61 --> BB210 : ..................
## 13 --> AA268 : ..................
##
##
## Placing remaining marker(s) at most likely position
## 61 --> BB210 : ..................
## 13 --> AA268 : ...................
##
## Estimating final genetic map using tol = 10E-5.LG5_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 65 BB186 0.00
## 247 CC124 6.81
## 282 MgSTS40 16.84
## 371 MgSTS586 38.26
## 113 CB230 44.78
## 129 BD316C 46.74
## 5 AA378 54.37
## 141 BD173 60.99
## 86 CA264 65.87
## 294 MgSTS245 76.79
## 234 CC342 88.88
## 157 AA454C 97.06
## 19 AA163 106.38
## 192 BC506 122.56
## 332 MgSTS282A 141.75
## 333 MgSTS255 145.80
## 152 AA118C 173.84
##
## 17 markers log-likelihood: -2227.567
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------
## | | 61 | 13 |
## |-----|-----|-----|
## | | | |
## | 65 | | |
## | | | |
## | 247 | | |
## | | | |
## | 282 | | |
## | | | |
## | 371 | | |
## | | | |
## | 113 | | |
## | | *** | |
## | 129 | | |
## | | | |
## | 5 | | |
## | | | |
## | 141 | | |
## | | | |
## | 86 | | |
## | | | |
## | 294 | | |
## | | | *** |
## | 234 | | |
## | | | ** |
## | 157 | | |
## | | | |
## | 19 | | |
## | | | |
## | 192 | | |
## | | | |
## | 332 | | |
## | | | |
## | 333 | | |
## | | | |
## | 152 | | |
## | | | |
## -------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_5rm <- make_seq(LG5_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 65 BB186 0.00
## 247 CC124 6.84
## 282 MgSTS40 16.82
## 371 MgSTS586 38.15
## 113 CB230 44.25
## 61 BB210 45.88
## 129 BD316C 47.70
## 5 AA378 55.82
## 141 BD173 62.53
## 86 CA264 67.46
## 294 MgSTS245 78.78
## 13 AA268 87.89
## 234 CC342 95.55
## 157 AA454C 102.90
## 19 AA163 112.22
## 192 BC506 128.41
## 332 MgSTS282A 147.59
## 333 MgSTS255 151.64
## 152 AA118C 179.68
##
## 19 markers log-likelihood: -2330.963HGL5<-rf_graph_table(Ligação_grupo_5rm, axis.cex=.6, inter=FALSE)
GL5<-Ligação_grupo_5rmORDERING MARKERS THE NEXT LINKAGE GROUP
set_map_fun(type = "kosambi")
LG6_f2 <- make_seq(LGs_f2, 6)
LG6_f2##
## Number of markers: 51
## Too many markers - not printing their names
##
## Parameters not estimated.LG6_rcd_f2 <- rcd(LG6_f2)##
## order obtained using RCD algorithm:
##
## 224 309 306 267 402 418 9 51 20 12 11 181 139 274 401 354 411 359 273 264 292 417 280 412 254 268 186 106 143 39 240 83 230 99 398 399 343 272 342 389 297 414 351 344 195 6 204 246 213 312 150
##
## calculating multipoint map using tol = 1e-04 .LG6_f2_ord <- order_seq(input.seq = LG6_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 224 309 306 267 402 418 9 51 20 12 11 181 139 274 401 354 411 359 273 264 292 417 280 412 254 268 186 106 143 39 240 83 230 99 398 399 343 272 342 389 297 414 351 344 195 6 204 246 213 312 150
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 99 --> CA152C : ......
## 389 --> MgSTS606 : .......
## 6 --> AA371C : ........
## 399 --> MgSTS504B : .........
## 412 --> MgSTS220 : ..........
## 398 --> MgSTS504A : ...........
## 411 --> MgSTS459 : ............
## 292 --> MgSTS229 : .............
## 267 --> MgSTS25 : ..............
## 280 --> MgSTS58 : ...............
## 273 --> MgSTS105 : ................
## 312 --> MgSTS480 : .................
## 401 --> MgSTS545 : .................
## 402 --> MgSTS542A : ..................
## 309 --> MgSTS529 : ...................
## 306 --> MgSTS508 : ....................
## 181 --> AAT230 : ....................
## 418 --> MgSTS440 : ....................
## 254 --> CC171C : ....................
## 343 --> MgSTS453 : .....................
## 264 --> MgSTS21 : .....................
## 414 --> MgSTS467 : ......................
## 354 --> MgSTS314 : .......................
## 344 --> MgSTS456 : ........................
## 297 --> MgSTS323 : .........................
## 417 --> MgSTS431 : ..........................
## 342 --> MgSTS426 : ...........................
## 186 --> AAT300 : ............................
## 351 --> MgSTS430 : .............................
## 359 --> MgSTS320 : .............................
## 106 --> CB333 : ..............................
## 83 --> CA283 : ..............................
## 9 --> AA311 : ..............................
## 11 --> AA277 : ..............................
## 39 --> BA222 : ...............................
## 139 --> BD179 : ...............................
## 204 --> BC243 : ...............................
## 213 --> BC125 : ...............................
## 230 --> CC381 : ...............................
## 20 --> AA158 : ................................
## 12 --> AA270 : .................................
## 51 --> BA117 : .................................
## 143 --> BD169 : .................................
## 195 --> BC392 : ..................................
## 240 --> CC262 : ...................................
## 246 --> CC126 : ....................................
##
## LOD threshold = 3
##
## Positioned markers: 224 309 267 402 401 354 274 411 359 11 20 273 264 280 417 292 412 143 254 230 99 186 268 240 398 342 272 399 389 297 414 344 195 6 150
##
## Markers not placed on the map: 306 418 9 51 12 181 139 106 39 83 343 351 204 246 213 312
##
##
## Calculating LOD-Scores
## 306 --> MgSTS508 : ....................................
## 418 --> MgSTS440 : ....................................
## 9 --> AA311 : ....................................
## 51 --> BA117 : ....................................
## 12 --> AA270 : ....................................
## 181 --> AAT230 : ....................................
## 139 --> BD179 : ....................................
## 106 --> CB333 : ....................................
## 39 --> BA222 : ....................................
## 83 --> CA283 : ....................................
## 343 --> MgSTS453 : ....................................
## 351 --> MgSTS430 : ....................................
## 204 --> BC243 : ....................................
## 246 --> CC126 : ....................................
## 213 --> BC125 : ....................................
## 312 --> MgSTS480 : ....................................
##
##
## Placing remaining marker(s) at most likely position
## 204 --> BC243 : ....................................
## 181 --> AAT230 : .....................................
## 139 --> BD179 : ......................................
## 351 --> MgSTS430 : .......................................
## 418 --> MgSTS440 : ........................................
## 312 --> MgSTS480 : .........................................
## 246 --> CC126 : ..........................................
## 106 --> CB333 : ...........................................
## 9 --> AA311 : ............................................
## 213 --> BC125 : .............................................
## 12 --> AA270 : ..............................................
## 51 --> BA117 : ...............................................
## 343 --> MgSTS453 : ................................................
## 39 --> BA222 : .................................................
## 306 --> MgSTS508 : ..................................................
## 83 --> CA283 : ...................................................
##
## Estimating final genetic map using tol = 10E-5.LG6_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 224 CC457 0.00
## 309 MgSTS529 8.18
## 267 MgSTS25 26.29
## 402 MgSTS542A 33.19
## 401 MgSTS545 44.59
## 354 MgSTS314 46.71
## 274 MgSTS120 49.93
## 411 MgSTS459 54.82
## 359 MgSTS320 58.46
## 11 AA277 64.52
## 20 AA158 70.05
## 273 MgSTS105 77.65
## 264 MgSTS21 79.66
## 280 MgSTS58 93.23
## 417 MgSTS431 95.32
## 292 MgSTS229 97.24
## 412 MgSTS220 105.24
## 143 BD169 112.15
## 254 CC171C 116.66
## 230 CC381 124.30
## 99 CA152C 128.10
## 186 AAT300 132.22
## 268 MgSTS22 134.83
## 240 CC262 140.79
## 398 MgSTS504A 145.46
## 342 MgSTS426 154.72
## 272 MgSTS28 156.95
## 399 MgSTS504B 158.37
## 389 MgSTS606 164.35
## 297 MgSTS323 165.91
## 414 MgSTS467 167.09
## 344 MgSTS456 171.90
## 195 BC392 176.90
## 6 AA371C 189.78
## 150 BD55 243.62
##
## 35 markers log-likelihood: -3470.561
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------------------------
## | | 306 | 418 | 9 | 51 | 12 | 181 | 139 | 106 | 39 | 83 | 343 | 351 | 204 | 246 | 213 | 312 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | | | *** | | | | | | | | | | | | ** | |
## | 224 | | | | | | | | | | | | | | | | |
## | | ** | | | | | | | | | | | | | | | |
## | 309 | | | | | | | | | | | | | | | | |
## | | *** | *** | * | | | | | | | | | | | | | |
## | 267 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 402 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 401 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 354 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 274 | | | | | | | | | | | | | | | | |
## | | | | | | | | *** | | | | | | | | | |
## | 411 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 359 | | | | | | | | | | | | | | | | |
## | | | | | *** | ** | *** | | | | | | | | | | |
## | 11 | | | | | | | | | | | | | | | | |
## | | | | | ** | *** | | | | | | | | | | | |
## | 20 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 273 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 264 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 280 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 417 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 292 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 412 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 143 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 254 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | * | | | | | | | |
## | 230 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 99 | | | | | | | | | | | | | | | | |
## | | | | | | | | | * | * | | | | | | | |
## | 186 | | | | | | | | | | | | | | | | |
## | | | | | | | | | *** | *** | | | | | | | |
## | 268 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | ** | *** | | | | | | |
## | 240 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | ** | ** | | | | | | |
## | 398 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | *** | | |
## | 342 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 272 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | *** | | | | | |
## | 399 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | ** | | | | | |
## | 389 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 297 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 414 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | *** | | | | |
## | 344 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 195 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | |
## | 6 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | *** | * | ** | *** |
## | 150 | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | *** | * |
## -------------------------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_6 <- make_seq(LG6_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 224 CC457 0.00
## 306 MgSTS508 7.93
## 309 MgSTS529 9.13
## 9 AA311 17.03
## 418 MgSTS440 24.56
## 267 MgSTS25 34.84
## 402 MgSTS542A 41.57
## 401 MgSTS545 52.90
## 354 MgSTS314 54.93
## 274 MgSTS120 58.00
## 139 BD179 60.07
## 411 MgSTS459 63.66
## 359 MgSTS320 67.28
## 181 AAT230 77.60
## 51 BA117 90.55
## 11 AA277 97.76
## 12 AA270 102.56
## 20 AA158 110.83
## 273 MgSTS105 117.93
## 264 MgSTS21 119.98
## 280 MgSTS58 133.54
## 417 MgSTS431 135.64
## 292 MgSTS229 137.55
## 412 MgSTS220 145.56
## 143 BD169 152.46
## 254 CC171C 156.98
## 230 CC381 164.61
## 99 CA152C 168.41
## 186 AAT300 172.62
## 106 CB333 173.75
## 268 MgSTS22 176.66
## 39 BA222 180.62
## 83 CA283 186.81
## 240 CC262 186.82
## 398 MgSTS504A 192.70
## 246 CC126 200.56
## 342 MgSTS426 211.42
## 272 MgSTS28 213.71
## 343 MgSTS453 215.09
## 399 MgSTS504B 215.46
## 389 MgSTS606 221.35
## 297 MgSTS323 222.75
## 414 MgSTS467 224.30
## 351 MgSTS430 224.59
## 344 MgSTS456 229.66
## 195 BC392 234.61
## 6 AA371C 247.38
## 204 BC243 269.98
## 312 MgSTS480 304.87
## 213 BC125 346.48
## 150 BD55 388.22
##
## 51 markers log-likelihood: -4895.778#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_6, axis.cex=.6, inter=FALSE)
LG6seq_f2_rm <- drop_marker(Ligação_grupo_6, c(39,359,106, 150, 6, 181))
LG6_rcd_f2_rm <- rcd(LG6seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 224 309 306 267 402 418 9 51 20 12 11 139 274 401 354 411 273 264 292 417 280 412 99 254 143 268 186 230 83 240 398 399 343 272 342 389 297 414 351 344 195 246 213 204 312
##
## calculating multipoint map using tol = 1e-04 .LG6_f2_ord_rm <- order_seq(input.seq = LG6_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 224 309 306 267 402 418 9 51 20 12 11 139 274 401 354 411 273 264 292 417 280 412 99 254 143 268 186 230 83 240 398 399 343 272 342 389 297 414 351 344 195 246 213 204 312
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 268 --> MgSTS22 : ......
## 389 --> MgSTS606 : .......
## 274 --> MgSTS120 : ........
## 399 --> MgSTS504B : ........
## 412 --> MgSTS220 : .........
## 398 --> MgSTS504A : .........
## 411 --> MgSTS459 : ..........
## 292 --> MgSTS229 : ..........
## 267 --> MgSTS25 : ...........
## 280 --> MgSTS58 : ............
## 273 --> MgSTS105 : .............
## 401 --> MgSTS545 : ..............
## 402 --> MgSTS542A : ...............
## 309 --> MgSTS529 : ................
## 306 --> MgSTS508 : .................
## 418 --> MgSTS440 : .................
## 254 --> CC171C : .................
## 343 --> MgSTS453 : ..................
## 264 --> MgSTS21 : ..................
## 414 --> MgSTS467 : ..................
## 354 --> MgSTS314 : ...................
## 344 --> MgSTS456 : ....................
## 297 --> MgSTS323 : .....................
## 417 --> MgSTS431 : ......................
## 342 --> MgSTS426 : .......................
## 186 --> AAT300 : ........................
## 351 --> MgSTS430 : .........................
## 83 --> CA283 : .........................
## 9 --> AA311 : .........................
## 11 --> AA277 : .........................
## 213 --> BC125 : ..........................
## 204 --> BC243 : ..........................
## 230 --> CC381 : ...........................
## 20 --> AA158 : ............................
## 12 --> AA270 : .............................
## 51 --> BA117 : .............................
## 143 --> BD169 : ..............................
## 195 --> BC392 : ...............................
## 240 --> CC262 : ................................
## 246 --> CC126 : .................................
##
## LOD threshold = 3
##
## Positioned markers: 224 309 267 402 401 354 139 11 51 20 273 280 417 292 143 254 230 99 186 268 240 398 342 272 399 389 297 414 344 195 204 312
##
## Markers not placed on the map: 306 418 9 12 274 411 264 412 83 343 351 246 213
##
##
## Calculating LOD-Scores
## 306 --> MgSTS508 : .................................
## 418 --> MgSTS440 : .................................
## 9 --> AA311 : .................................
## 12 --> AA270 : .................................
## 274 --> MgSTS120 : .................................
## 411 --> MgSTS459 : .................................
## 264 --> MgSTS21 : .................................
## 412 --> MgSTS220 : .................................
## 83 --> CA283 : .................................
## 343 --> MgSTS453 : .................................
## 351 --> MgSTS430 : .................................
## 246 --> CC126 : .................................
## 213 --> BC125 : .................................
##
##
## Placing remaining marker(s) at most likely position
## 412 --> MgSTS220 : .................................
## 274 --> MgSTS120 : ..................................
## 264 --> MgSTS21 : ...................................
## 418 --> MgSTS440 : ....................................
## 351 --> MgSTS430 : .....................................
## 246 --> CC126 : ......................................
## 213 --> BC125 : .......................................
## 9 --> AA311 : ........................................
## 343 --> MgSTS453 : .........................................
## 306 --> MgSTS508 : ..........................................
## 12 --> AA270 : ...........................................
## 411 --> MgSTS459 : ............................................
## 83 --> CA283 : .............................................
##
## Estimating final genetic map using tol = 10E-5.LG6_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 224 CC457 0.00
## 309 MgSTS529 8.13
## 267 MgSTS25 26.08
## 402 MgSTS542A 32.95
## 401 MgSTS545 44.31
## 354 MgSTS314 46.39
## 139 BD179 50.82
## 11 AA277 57.84
## 51 BA117 59.79
## 20 AA158 70.12
## 273 MgSTS105 77.61
## 280 MgSTS58 92.21
## 417 MgSTS431 94.30
## 292 MgSTS229 96.29
## 143 BD169 110.12
## 254 CC171C 114.46
## 230 CC381 122.01
## 99 CA152C 125.77
## 186 AAT300 129.89
## 268 MgSTS22 132.50
## 240 CC262 138.46
## 398 MgSTS504A 143.13
## 342 MgSTS426 152.39
## 272 MgSTS28 154.61
## 399 MgSTS504B 156.04
## 389 MgSTS606 162.02
## 297 MgSTS323 163.57
## 414 MgSTS467 164.75
## 344 MgSTS456 169.79
## 195 BC392 174.44
## 204 BC243 184.35
## 312 MgSTS480 219.08
##
## 32 markers log-likelihood: -3282.637
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------
## | | 306 | 418 | 9 | 12 | 274 | 411 | 264 | 412 | 83 | 343 | 351 | 246 | 213 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | | | *** | | | | | | | | | | |
## | 224 | | | | | | | | | | | | | |
## | | ** | | | | | | | | | | | | |
## | 309 | | | | | | | | | | | | | |
## | | *** | *** | * | | | | | | | | | | |
## | 267 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 402 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 401 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 354 | | | | | | | | | | | | | |
## | | | | | | *** | ** | | | | | | | |
## | 139 | | | | | | | | | | | | | |
## | | | | | | | *** | | | | | | | |
## | 11 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 51 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 20 | | | | | | | | | | | | | |
## | | | | | ** | | | | | | | | | |
## | 273 | | | | | | | | | | | | | |
## | | | | | *** | | | *** | | | | | | |
## | 280 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 417 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 292 | | | | | | | | | | | | | |
## | | | | | | | | | *** | | | | | |
## | 143 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 254 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 230 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 99 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 186 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 268 | | | | | | | | | | | | | |
## | | | | | | | | | | *** | | | | |
## | 240 | | | | | | | | | | | | | |
## | | | | | | | | | | ** | | | | |
## | 398 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | *** | |
## | 342 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 272 | | | | | | | | | | | | | |
## | | | | | | | | | | | *** | | | |
## | 399 | | | | | | | | | | | | | |
## | | | | | | | | | | | ** | | | |
## | 389 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 297 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 414 | | | | | | | | | | | | | |
## | | | | | | | | | | | | *** | | |
## | 344 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 195 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 204 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 312 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | *** |
## -------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_6rm <- make_seq(LG6_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 224 CC457 0.00
## 306 MgSTS508 7.93
## 309 MgSTS529 9.13
## 9 AA311 17.03
## 418 MgSTS440 24.56
## 267 MgSTS25 34.84
## 402 MgSTS542A 41.57
## 401 MgSTS545 52.90
## 354 MgSTS314 54.93
## 274 MgSTS120 58.01
## 139 BD179 60.18
## 411 MgSTS459 63.84
## 11 AA277 71.53
## 51 BA117 73.92
## 20 AA158 83.91
## 12 AA270 92.01
## 273 MgSTS105 98.24
## 264 MgSTS21 100.32
## 280 MgSTS58 113.87
## 417 MgSTS431 115.97
## 292 MgSTS229 117.89
## 412 MgSTS220 125.89
## 143 BD169 132.80
## 254 CC171C 137.32
## 230 CC381 144.95
## 99 CA152C 148.76
## 186 AAT300 152.88
## 268 MgSTS22 155.49
## 83 CA283 162.74
## 240 CC262 163.00
## 398 MgSTS504A 168.78
## 246 CC126 176.65
## 342 MgSTS426 187.50
## 272 MgSTS28 189.80
## 343 MgSTS453 191.17
## 399 MgSTS504B 191.55
## 389 MgSTS606 197.43
## 297 MgSTS323 198.83
## 414 MgSTS467 200.38
## 351 MgSTS430 200.68
## 344 MgSTS456 205.98
## 195 BC392 210.59
## 204 BC243 220.50
## 312 MgSTS480 254.80
## 213 BC125 300.01
##
## 45 markers log-likelihood: -4203.523GL6<-Ligação_grupo_6rm
HGL6<-rf_graph_table(Ligação_grupo_6rm, axis.cex=.6, inter=FALSE)
#ORDERING MARKERS THE NEXT LINKAGE GROUP
set_map_fun(type = "kosambi")
LG7_f2 <- make_seq(LGs_f2, 7)
LG7_f2##
## Number of markers: 32
## Markers in the sequence:
## AA246 BA372 BA314 BA158 BB167 CA305 CA210 CA122 CB272 BD189C AAT217 AAT39
## AAT211 AAT296 CYCB AAT242 CC450 CC359 CC338C MgSTS59 MgSTS69 MgSTS31
## MgSTS76 MgSTS330 MgSTS381 MgSTS571 MgSTS590 MgSTS537 MgSTS538 MgSTS563
## MgSTS504C MgSTS621
##
## Parameters not estimated.LG7_rcd_f2 <- rcd(LG7_f2)##
## order obtained using RCD algorithm:
##
## 46 68 324 14 253 409 233 166 36 151 352 374 103 327 318 368 400 363 110 180 173 172 225 80 303 187 378 316 373 94 34 188
##
## calculating multipoint map using tol = 1e-04 .LG7_f2_ord <- order_seq(input.seq = LG7_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 46 68 324 14 253 409 233 166 36 151 352 374 103 327 318 368 400 363 110 180 173 172 225 80 303 187 378 316 373 94 34 188
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 172 --> AAT39 : ......
## 378 --> MgSTS563 : .......
## 400 --> MgSTS504C : ........
## 173 --> AAT211 : .........
## 409 --> MgSTS621 : ..........
## 151 --> BD189C : ...........
## 374 --> MgSTS538 : ............
## 373 --> MgSTS537 : .............
## 166 --> AAT217 : ..............
## 363 --> MgSTS571 : ..............
## 187 --> CYCB : ...............
## 316 --> MgSTS69 : ................
## 253 --> CC338C : ................
## 318 --> MgSTS31 : .................
## 180 --> AAT296 : ..................
## 352 --> MgSTS381 : ...................
## 303 --> MgSTS59 : ....................
## 327 --> MgSTS330 : ....................
## 324 --> MgSTS76 : ....................
## 110 --> CB272 : .....................
## 103 --> CA122 : ......................
## 94 --> CA210 : .......................
## 14 --> AA246 : .......................
## 233 --> CC359 : .......................
## 68 --> BB167 : ........................
## 34 --> BA372 : ........................
## 225 --> CC450 : .........................
##
## LOD threshold = 3
##
## Positioned markers: 46 324 409 233 253 374 352 318 103 151 36 110 363 400 368 180 173 172 80 187 188 378 373 34
##
## Markers not placed on the map: 68 14 166 327 225 303 316 94
##
##
## Calculating LOD-Scores
## 68 --> BB167 : .........................
## 14 --> AA246 : .........................
## 166 --> AAT217 : .........................
## 327 --> MgSTS330 : .........................
## 225 --> CC450 : .........................
## 303 --> MgSTS59 : .........................
## 316 --> MgSTS69 : .........................
## 94 --> CA210 : .........................
##
##
## Placing remaining marker(s) at most likely position
## 166 --> AAT217 : .........................
## 94 --> CA210 : ..........................
## 303 --> MgSTS59 : ...........................
## 14 --> AA246 : ............................
## 68 --> BB167 : .............................
## 225 --> CC450 : ..............................
## 327 --> MgSTS330 : ...............................
## 316 --> MgSTS69 : ................................
##
## Estimating final genetic map using tol = 10E-5.LG7_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 46 BA158 0.00
## 324 MgSTS76 18.74
## 409 MgSTS621 35.42
## 233 CC359 38.88
## 253 CC338C 51.79
## 374 MgSTS538 63.07
## 352 MgSTS381 72.44
## 318 MgSTS31 80.50
## 103 CA122 84.27
## 151 BD189C 95.75
## 36 BA314 107.39
## 110 CB272 119.62
## 363 MgSTS571 125.21
## 400 MgSTS504C 127.62
## 368 MgSTS590 129.86
## 180 AAT296 150.60
## 173 AAT211 158.29
## 172 AAT39 161.70
## 80 CA305 172.35
## 187 CYCB 179.72
## 188 AAT242 187.95
## 378 MgSTS563 205.07
## 373 MgSTS537 220.62
## 34 BA372 230.16
##
## 24 markers log-likelihood: -3214.938
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------
## | | 68 | 14 | 166 | 327 | 225 | 303 | 316 | 94 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | | | | | | | | |
## | 46 | | | | | | | | |
## | | *** | *** | | | | | | |
## | 324 | | | | | | | | |
## | | * | * | | | | | | |
## | 409 | | | | | | | | |
## | | | | | | | | | |
## | 233 | | | | | | | | |
## | | | | *** | | | | | |
## | 253 | | | | | | | | |
## | | | | | | | | | |
## | 374 | | | | | | | | |
## | | | | | *** | | | | |
## | 352 | | | | | | | | |
## | | | | | ** | | | | |
## | 318 | | | | | | | | |
## | | | | | | | | | |
## | 103 | | | | | | | | |
## | | | | | | | | | |
## | 151 | | | | | | | | |
## | | | | | | | | | |
## | 36 | | | | | | | | |
## | | | | | | | | | |
## | 110 | | | | | | | | |
## | | | | | | | | | |
## | 363 | | | | | | | | |
## | | | | | | | | | |
## | 400 | | | | | | | | |
## | | | | | | | | | |
## | 368 | | | | | | | | |
## | | | | | | | | | |
## | 180 | | | | | | | | |
## | | | | | | | | | |
## | 173 | | | | | | | | |
## | | | | | | | | | |
## | 172 | | | | | | | | |
## | | | | | | *** | * | | |
## | 80 | | | | | | | | |
## | | | | | | ** | *** | | |
## | 187 | | | | | | | | |
## | | | | | | | | | |
## | 188 | | | | | | | | |
## | | | | | | | | ** | |
## | 378 | | | | | | | | |
## | | | | | | | | *** | * |
## | 373 | | | | | | | | |
## | | | | | | | | | *** |
## | 34 | | | | | | | | |
## | | | | | | | | | |
## -------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_7 <- make_seq(LG7_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 46 BA158 0.00
## 68 BB167 18.12
## 14 AA246 20.48
## 324 MgSTS76 24.56
## 409 MgSTS621 39.53
## 233 CC359 43.69
## 166 AAT217 51.68
## 253 CC338C 64.15
## 374 MgSTS538 75.08
## 327 MgSTS330 79.93
## 352 MgSTS381 84.01
## 318 MgSTS31 91.18
## 103 CA122 94.99
## 151 BD189C 106.47
## 36 BA314 118.11
## 110 CB272 130.34
## 363 MgSTS571 135.93
## 400 MgSTS504C 138.35
## 368 MgSTS590 140.58
## 180 AAT296 161.35
## 173 AAT211 169.06
## 172 AAT39 172.44
## 225 CC450 182.89
## 80 CA305 188.58
## 303 MgSTS59 192.41
## 187 CYCB 199.60
## 188 AAT242 207.54
## 378 MgSTS563 224.50
## 316 MgSTS69 225.15
## 373 MgSTS537 240.87
## 94 CA210 245.40
## 34 BA372 252.01
##
## 32 markers log-likelihood: -3762.724#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
HGL8<-rf_graph_table(Ligação_grupo_7, axis.cex=.6, inter=FALSE)
GL8<-Ligação_grupo_7ORDERING MARKERS THE NEXT LINKAGE GROUP
set_map_fun(type = "kosambi")
LG8_f2 <- make_seq(LGs_f2, 8)
LG8_f2##
## Number of markers: 26
## Markers in the sequence:
## AA167 AA95 BA445 BA400 BA311 BB218 BB176 CA261 CA217 CA196 CA167 CB115
## BA396C AAT222 BC108 BC83 CC540 CC402 LFY MgSTS468 MgSTS638 MgSTS536
## MgSTS558 MgSTS611 MgSTS600 MgSTS470
##
## Parameters not estimated.LG8_rcd_f2 <- rcd(LG8_f2)##
## order obtained using RCD algorithm:
##
## 227 174 375 215 27 222 87 29 17 67 122 96 23 37 384 257 367 160 59 214 387 415 381 311 98 93
##
## calculating multipoint map using tol = 1e-04 .LG8_f2_ord <- order_seq(input.seq = LG8_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 227 174 375 215 27 222 87 29 17 67 122 96 23 37 384 257 367 160 59 214 387 415 381 311 98 93
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
|
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##
##
##
## Running try algorithm
## 381 --> MgSTS558 : ......
## 174 --> AAT222 : ......
## 384 --> MgSTS611 : ......
## 387 --> MgSTS600 : .......
## 160 --> BA396C : ........
## 375 --> MgSTS536 : .........
## 415 --> MgSTS470 : ..........
## 311 --> MgSTS468 : ...........
## 257 --> LFY : ............
## 367 --> MgSTS638 : .............
## 67 --> BB176 : ..............
## 122 --> CB115 : ...............
## 96 --> CA196 : ................
## 98 --> CA167 : ................
## 23 --> AA95 : ................
## 27 --> BA445 : .................
## 29 --> BA400 : .................
## 215 --> BC83 : .................
## 59 --> BB218 : .................
## 17 --> AA167 : ..................
## 222 --> CC540 : ..................
##
## LOD threshold = 3
##
## Positioned markers: 227 122 67 375 23 37 384 257 87 367 160 214 59 387 415 311 93
##
## Markers not placed on the map: 174 215 27 222 29 17 96 381 98
##
##
## Calculating LOD-Scores
## 174 --> AAT222 : ..................
## 215 --> BC83 : ..................
## 27 --> BA445 : ..................
## 222 --> CC540 : ..................
## 29 --> BA400 : ..................
## 17 --> AA167 : ..................
## 96 --> CA196 : ..................
## 381 --> MgSTS558 : ..................
## 98 --> CA167 : ..................
##
##
## Placing remaining marker(s) at most likely position
## 381 --> MgSTS558 : ..................
## 174 --> AAT222 : ...................
## 96 --> CA196 : ....................
## 222 --> CC540 : .....................
## 215 --> BC83 : ......................
## 27 --> BA445 : .......................
## 29 --> BA400 : ........................
## 17 --> AA167 : .........................
## 98 --> CA167 : ..........................
##
## Estimating final genetic map using tol = 10E-5.LG8_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 227 CC402 0.00
## 122 CB115 10.93
## 67 BB176 17.01
## 375 MgSTS536 37.09
## 23 AA95 56.52
## 37 BA311 62.95
## 384 MgSTS611 67.90
## 257 LFY 72.73
## 87 CA261 80.48
## 367 MgSTS638 93.53
## 160 BA396C 108.82
## 214 BC108 118.76
## 59 BB218 122.39
## 387 MgSTS600 129.08
## 415 MgSTS470 130.26
## 311 MgSTS468 134.66
## 93 CA217 141.12
##
## 17 markers log-likelihood: -1940.694
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------
## | | 174 | 215 | 27 | 222 | 29 | 17 | 96 | 381 | 98 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | | | *** | | | | | | |
## | 227 | | | | | | | | | |
## | | | | | | ** | | * | | |
## | 122 | | | | | | | | | |
## | | | | | | ** | * | | | |
## | 67 | | | | | | | | | |
## | | *** | ** | ** | | *** | *** | *** | | |
## | 375 | | | | | | | | | |
## | | | *** | | * | | ** | | | |
## | 23 | | | | | | | | | |
## | | | | | | | | | | |
## | 37 | | | | | | | | | |
## | | | | | | | | | | |
## | 384 | | | | | | | | | |
## | | | | | | | | | | |
## | 257 | | | | | | | | | |
## | | | | | | | | | | |
## | 87 | | | | | | | | | |
## | | | | | *** | | ** | | | |
## | 367 | | | | | | | | | |
## | | | | | | | | | | |
## | 160 | | | | | | | | | |
## | | | | | | | | | | |
## | 214 | | | | | | | | | |
## | | | | | | | | | | |
## | 59 | | | | | | | | | |
## | | | | | | | | | | |
## | 387 | | | | | | | | | |
## | | | | | | | | | | |
## | 415 | | | | | | | | | |
## | | | | | | | | | | |
## | 311 | | | | | | | | | |
## | | | | | | | | | *** | *** |
## | 93 | | | | | | | | | |
## | | | | | | | | | | ** |
## -------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_8 <- make_seq(LG8_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 27 BA445 0.00
## 227 CC402 20.42
## 122 CB115 30.50
## 67 BB176 36.60
## 29 BA400 42.83
## 96 CA196 49.42
## 215 BC83 66.85
## 174 AAT222 81.06
## 375 MgSTS536 93.91
## 23 AA95 113.29
## 37 BA311 119.84
## 384 MgSTS611 124.88
## 257 LFY 129.72
## 87 CA261 138.37
## 17 AA167 146.37
## 222 CC540 153.81
## 367 MgSTS638 170.93
## 160 BA396C 186.26
## 214 BC108 196.22
## 59 BB218 199.87
## 387 MgSTS600 206.58
## 415 MgSTS470 207.81
## 311 MgSTS468 212.01
## 381 MgSTS558 213.65
## 93 CA217 217.37
## 98 CA167 218.82
##
## 26 markers log-likelihood: -2759.219#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_8, axis.cex=.6, inter=FALSE)
LG8seq_f2_rm <- drop_marker(Ligação_grupo_8, c(215, 17, 29,122, 227,67))
LG8_rcd_f2_rm <- rcd(LG8seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 27 174 375 96 222 87 23 37 384 257 367 160 214 59 387 415 311 381 93 98
##
## calculating multipoint map using tol = 1e-04 .LG8_f2_ord_rm <- order_seq(input.seq = LG8_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 27 174 375 96 222 87 23 37 384 257 367 160 214 59 387 415 311 381 93 98
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
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##
##
##
## Running try algorithm
## 381 --> MgSTS558 : ......
## 174 --> AAT222 : .......
## 384 --> MgSTS611 : .......
## 160 --> BA396C : .......
## 375 --> MgSTS536 : ........
## 415 --> MgSTS470 : .........
## 311 --> MgSTS468 : ..........
## 367 --> MgSTS638 : ..........
## 96 --> CA196 : ...........
## 23 --> AA95 : ............
## 37 --> BA311 : ............
## 59 --> BB218 : .............
## 93 --> CA217 : ..............
## 214 --> BC108 : ..............
## 222 --> CC540 : ...............
##
## LOD threshold = 3
##
## Positioned markers: 27 375 96 222 87 37 257 367 160 214 59 387 415 381 98
##
## Markers not placed on the map: 174 23 384 311 93
##
##
## Calculating LOD-Scores
## 174 --> AAT222 : ................
## 23 --> AA95 : ................
## 384 --> MgSTS611 : ................
## 311 --> MgSTS468 : ................
## 93 --> CA217 : ................
##
##
## Placing remaining marker(s) at most likely position
## 23 --> AA95 : ................
## 384 --> MgSTS611 : .................
## 174 --> AAT222 : ..................
## 311 --> MgSTS468 : ...................
## 93 --> CA217 : ....................
##
## Estimating final genetic map using tol = 10E-5.LG8_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 27 BA445 0.00
## 375 MgSTS536 23.02
## 96 CA196 39.55
## 222 CC540 47.01
## 87 CA261 56.68
## 37 BA311 64.41
## 257 LFY 71.87
## 367 MgSTS638 79.49
## 160 BA396C 95.20
## 214 BC108 105.28
## 59 BB218 108.96
## 387 MgSTS600 115.71
## 415 MgSTS470 116.97
## 381 MgSTS558 121.21
## 98 CA167 126.59
##
## 15 markers log-likelihood: -1787.972
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------
## | | 174 | 23 | 384 | 311 | 93 |
## |-----|-----|-----|-----|-----|-----|
## | | | | | | |
## | 27 | | | | | |
## | | *** | | | | |
## | 375 | | | | | |
## | | | | | | |
## | 96 | | | | | |
## | | | | | | |
## | 222 | | | | | |
## | | | | | | |
## | 87 | | | | | |
## | | | *** | | | |
## | 37 | | | | | |
## | | | | *** | | |
## | 257 | | | | | |
## | | | | | | |
## | 367 | | | | | |
## | | | | | | |
## | 160 | | | | | |
## | | | | | | |
## | 214 | | | | | |
## | | | | | | |
## | 59 | | | | | |
## | | | | | | |
## | 387 | | | | | |
## | | | | | | |
## | 415 | | | | | |
## | | | | | * | |
## | 381 | | | | | |
## | | | | | *** | *** |
## | 98 | | | | | |
## | | | | | | ** |
## -------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_8rm <- make_seq(LG8_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 27 BA445 0.00
## 174 AAT222 23.66
## 375 MgSTS536 36.54
## 96 CA196 53.44
## 222 CC540 59.59
## 87 CA261 68.49
## 23 AA95 71.98
## 37 BA311 78.28
## 384 MgSTS611 83.01
## 257 LFY 88.28
## 367 MgSTS638 96.08
## 160 BA396C 112.03
## 214 BC108 122.01
## 59 BB218 125.66
## 387 MgSTS600 132.38
## 415 MgSTS470 133.63
## 381 MgSTS558 137.85
## 311 MgSTS468 139.38
## 98 CA167 144.62
## 93 CA217 145.06
##
## 20 markers log-likelihood: -2203.66HGL9<-rf_graph_table(Ligação_grupo_8rm, axis.cex=.6, inter=FALSE)
GL9<-Ligação_grupo_8rmORDERING MARKERS THE NEXT LINKAGE GROUP
set_map_fun(type = "kosambi")
LG9_f2 <- make_seq(LGs_f2, 9)
LG9_f2##
## Number of markers: 29
## Markers in the sequence:
## BA394 BA175 BB182 CA378 CA140 CB216 BD242 BD143 AA296C BA245C AAT233
## AAT272 AAT308 AAT364 BC546 BC478 BC388 BC376 BC330 BC266 BC219 CC149 CC114
## MgSTS36 MgSTS437 MgSTS113 MgSTS282B MgSTS548 MgSTS438
##
## Parameters not estimated.LG9_rcd_f2 <- rcd(LG9_f2)##
## order obtained using RCD algorithm:
##
## 66 101 114 392 298 78 154 201 331 382 314 183 185 44 189 158 300 144 198 196 136 203 248 30 176 194 205 242 182
##
## calculating multipoint map using tol = 1e-04 .LG9_f2_ord <- order_seq(input.seq = LG9_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 66 101 114 392 298 78 154 201 331 382 314 183 185 44 189 158 300 144 198 196 136 203 248 30 176 194 205 242 182
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 154 --> AA296C : ......
## 158 --> BA245C : .......
## 300 --> MgSTS437 : .......
## 392 --> MgSTS438 : ........
## 298 --> MgSTS36 : .........
## 183 --> AAT308 : .........
## 331 --> MgSTS282B : ..........
## 185 --> AAT364 : ...........
## 314 --> MgSTS113 : ............
## 382 --> MgSTS548 : ............
## 176 --> AAT233 : .............
## 101 --> CA140 : ..............
## 78 --> CA378 : ..............
## 144 --> BD143 : ..............
## 136 --> BD242 : ..............
## 198 --> BC376 : ...............
## 196 --> BC388 : ................
## 194 --> BC478 : ................
## 205 --> BC219 : ................
## 248 --> CC114 : ................
## 242 --> CC149 : ................
## 114 --> CB216 : ................
## 44 --> BA175 : .................
## 30 --> BA394 : .................
##
## LOD threshold = 3
##
## Positioned markers: 66 114 392 154 201 176 203 300 198 189 136 183 185 382 331 182
##
## Markers not placed on the map: 101 298 78 314 44 158 144 196 248 30 194 205 242
##
##
## Calculating LOD-Scores
## 101 --> CA140 : .................
## 298 --> MgSTS36 : .................
## 78 --> CA378 : .................
## 314 --> MgSTS113 : .................
## 44 --> BA175 : .................
## 158 --> BA245C : .................
## 144 --> BD143 : .................
## 196 --> BC388 : .................
## 248 --> CC114 : .................
## 30 --> BA394 : .................
## 194 --> BC478 : .................
## 205 --> BC219 : .................
## 242 --> CC149 : .................
##
##
## Placing remaining marker(s) at most likely position
## 158 --> BA245C : .................
## 196 --> BC388 : ..................
## 242 --> CC149 : ...................
## 314 --> MgSTS113 : ....................
## 194 --> BC478 : .....................
## 298 --> MgSTS36 : ......................
## 44 --> BA175 : .......................
## 248 --> CC114 : ........................
## 78 --> CA378 : .........................
## 205 --> BC219 : ..........................
## 144 --> BD143 : ...........................
## 101 --> CA140 : ............................
## 30 --> BA394 : .............................
##
## Estimating final genetic map using tol = 10E-5.LG9_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 66 BB182 0.00
## 114 CB216 13.41
## 392 MgSTS438 19.66
## 154 AA296C 31.81
## 201 BC330 37.66
## 176 AAT233 440.61
## 203 BC266 468.06
## 300 MgSTS437 487.22
## 198 BC376 496.03
## 189 BC546 503.19
## 136 BD242 510.56
## 183 AAT308 531.23
## 185 AAT364 544.04
## 382 MgSTS548 553.76
## 331 MgSTS282B 560.77
## 182 AAT272 594.26
##
## 16 markers log-likelihood: -2377.183
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------
## | | 101 | 298 | 78 | 314 | 44 | 158 | 144 | 196 | 248 | 30 | 194 | 205 | 242 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | ** | | | | | | | | | | | | |
## | 66 | | | | | | | | | | | | | |
## | | *** | | ** | | | | | | | | | | |
## | 114 | | | | | | | | | | | | | |
## | | | *** | *** | | | | | | | | | | |
## | 392 | | | | | | | | | | | | | |
## | | | ** | ** | | | | | | | | | | |
## | 154 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 201 | | | | | | | | | | | | | |
## | | | | | | | | | | | *** | *** | *** | * |
## | 176 | | | | | | | | | | | | | |
## | | | | | | | | | | *** | ** | | | |
## | 203 | | | | | | | | | | | | | |
## | | | | | | | | *** | | ** | | | | |
## | 300 | | | | | | | | | | | | | |
## | | | | | | ** | *** | ** | | | | | | |
## | 198 | | | | | | | | | | | | | |
## | | | | | | ** | | | | | | | | |
## | 189 | | | | | | | | | | | | | |
## | | | | | | *** | | | *** | | | | | |
## | 136 | | | | | | | | | | | | | |
## | | | | | * | | | | | | | | | |
## | 183 | | | | | | | | | | | | | |
## | | | | | *** | | | | | | | | | |
## | 185 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 382 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 331 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 182 | | | | | | | | | | | | | |
## | | | | | | | | | | | | ** | ** | *** |
## -------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_9 <- make_seq(LG9_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 66 BB182 0.00
## 101 CA140 3.40
## 114 CB216 13.60
## 78 CA378 16.31
## 298 MgSTS36 21.54
## 392 MgSTS438 22.16
## 154 AA296C 34.44
## 201 BC330 40.15
## 205 BC219 84.55
## 194 BC478 118.21
## 176 AAT233 162.27
## 30 BA394 198.91
## 248 CC114 204.29
## 203 BC266 212.22
## 144 BD143 234.57
## 300 MgSTS437 244.55
## 158 BA245C 251.07
## 44 BA175 255.72
## 198 BC376 256.77
## 189 BC546 263.51
## 196 BC388 269.58
## 136 BD242 277.93
## 183 AAT308 296.74
## 314 MgSTS113 301.44
## 185 AAT364 313.17
## 382 MgSTS548 322.59
## 331 MgSTS282B 329.69
## 182 AAT272 361.76
## 242 CC149 396.70
##
## 29 markers log-likelihood: -3520.665#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_9, axis.cex=.6, inter=FALSE)
LG9seq_f2_rm <- drop_marker(Ligação_grupo_9, c(176, 182, 242, 194, 205))
LG9_rcd_f2_rm <- rcd(LG9seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 66 101 114 392 298 78 154 201 331 382 314 183 185 44 189 158 300 144 198 196 136 203 248 30
##
## calculating multipoint map using tol = 1e-04 .LG9_f2_ord_rm <- order_seq(input.seq = LG9_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 66 101 114 392 298 78 154 201 331 382 314 183 185 44 189 158 300 144 198 196 136 203 248 30
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
|
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|
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|
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##
##
##
## Running try algorithm
## 158 --> BA245C : ......
## 300 --> MgSTS437 : ......
## 392 --> MgSTS438 : .......
## 298 --> MgSTS36 : ........
## 331 --> MgSTS282B : ........
## 185 --> AAT364 : .........
## 314 --> MgSTS113 : ..........
## 382 --> MgSTS548 : ..........
## 101 --> CA140 : ...........
## 78 --> CA378 : ...........
## 136 --> BD242 : ...........
## 189 --> BC546 : ............
## 198 --> BC376 : .............
## 196 --> BC388 : ..............
## 203 --> BC266 : ..............
## 248 --> CC114 : ...............
## 114 --> CB216 : ...............
## 44 --> BA175 : ................
## 201 --> BC330 : ................
##
## LOD threshold = 3
##
## Positioned markers: 66 114 392 154 201 331 382 185 183 144 300 198 189 136 203 30
##
## Markers not placed on the map: 101 298 78 314 44 158 196 248
##
##
## Calculating LOD-Scores
## 101 --> CA140 : .................
## 298 --> MgSTS36 : .................
## 78 --> CA378 : .................
## 314 --> MgSTS113 : .................
## 44 --> BA175 : .................
## 158 --> BA245C : .................
## 196 --> BC388 : .................
## 248 --> CC114 : .................
##
##
## Placing remaining marker(s) at most likely position
## 158 --> BA245C : .................
## 196 --> BC388 : ..................
## 248 --> CC114 : ...................
## 44 --> BA175 : ....................
## 314 --> MgSTS113 : .....................
## 298 --> MgSTS36 : ......................
## 78 --> CA378 : .......................
## 101 --> CA140 : ........................
##
## Estimating final genetic map using tol = 10E-5.LG9_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 66 BB182 0.00
## 114 CB216 13.41
## 392 MgSTS438 19.66
## 154 AA296C 31.81
## 201 BC330 37.75
## 331 MgSTS282B 60.71
## 382 MgSTS548 67.97
## 185 AAT364 77.83
## 183 AAT308 90.91
## 144 BD143 110.56
## 300 MgSTS437 120.71
## 198 BC376 130.20
## 189 BC546 137.63
## 136 BD242 145.34
## 203 BC266 169.54
## 30 BA394 187.64
##
## 16 markers log-likelihood: -2126.334
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------
## | | 101 | 298 | 78 | 314 | 44 | 158 | 196 | 248 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | ** | | | | | | | |
## | 66 | | | | | | | | |
## | | *** | | ** | | | | | |
## | 114 | | | | | | | | |
## | | | *** | *** | | | | | |
## | 392 | | | | | | | | |
## | | | ** | ** | | | | | |
## | 154 | | | | | | | | |
## | | | | | | | | | |
## | 201 | | | | | | | | |
## | | | | | | | | | |
## | 331 | | | | | | | | |
## | | | | | | | | | |
## | 382 | | | | | | | | |
## | | | | | | | | | |
## | 185 | | | | | | | | |
## | | | | | *** | | | | |
## | 183 | | | | | | | | |
## | | | | | * | *** | | | |
## | 144 | | | | | | | | |
## | | | | | | * | | | |
## | 300 | | | | | | | | |
## | | | | | | | *** | | |
## | 198 | | | | | | | | |
## | | | | | | | | | |
## | 189 | | | | | | | | |
## | | | | | | | | | |
## | 136 | | | | | | | | |
## | | | | | | | | *** | |
## | 203 | | | | | | | | |
## | | | | | | | | | *** |
## | 30 | | | | | | | | |
## | | | | | | | | | |
## -------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_9rm <- make_seq(LG9_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 66 BB182 0.00
## 101 CA140 3.41
## 114 CB216 13.61
## 78 CA378 16.32
## 298 MgSTS36 21.55
## 392 MgSTS438 22.16
## 154 AA296C 34.44
## 201 BC330 40.47
## 331 MgSTS282B 63.42
## 382 MgSTS548 70.78
## 185 AAT364 80.35
## 314 MgSTS113 92.17
## 183 AAT308 96.99
## 144 BD143 115.89
## 300 MgSTS437 125.98
## 158 BA245C 132.48
## 44 BA175 136.22
## 198 BC376 139.07
## 189 BC546 146.78
## 136 BD242 154.84
## 196 BC388 165.14
## 203 BC266 184.85
## 248 CC114 192.51
## 30 BA394 205.11
##
## 24 markers log-likelihood: -2670.875HGL12<-rf_graph_table(Ligação_grupo_9rm, axis.cex=.6, inter=FALSE)
GL12<-Ligação_grupo_9rmORDERING MARKERS THE NEXT LINKAGE GROUP
set_map_fun(type = "kosambi")
LG10_f2 <- make_seq(LGs_f2, 10)
LG10_f2##
## Number of markers: 21
## Markers in the sequence:
## BA334 BA145 BB198 CA315 CB172 CB126 CB55 CB263C AAT240 BC199 CC150 MgSTS55
## MgSTS45 MgSTS11 MgSTS68 MgSTS326 MgSTS419 MgSTS577 MgSTS104 MgSTS622
## MgSTS599
##
## Parameters not estimated.LG10_rcd_f2 <- rcd(LG10_f2)##
## order obtained using RCD algorithm:
##
## 117 35 390 284 285 407 416 123 79 164 281 121 170 410 207 63 383 304 330 48 241
##
## calculating multipoint map using tol = 1e-04 .LG10_f2_ord <- order_seq(input.seq = LG10_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 117 35 390 284 285 407 416 123 79 164 281 121 170 410 207 63 383 304 330 48 241
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 170 --> AAT240 : ......
## 164 --> CB263C : .......
## 390 --> MgSTS577 : ........
## 284 --> MgSTS45 : .........
## 383 --> MgSTS419 : ..........
## 410 --> MgSTS622 : ..........
## 416 --> MgSTS599 : ...........
## 285 --> MgSTS11 : ............
## 304 --> MgSTS68 : .............
## 330 --> MgSTS326 : .............
## 123 --> CB55 : ..............
## 48 --> BA145 : ...............
## 207 --> BC199 : ................
## 121 --> CB126 : .................
## 79 --> CA315 : ..................
## 35 --> BA334 : ..................
##
## LOD threshold = 3
##
## Positioned markers: 117 35 390 284 285 407 416 123 164 281 121 170 410 330 48 241 207 63
##
## Markers not placed on the map: 79 383 304
##
##
## Calculating LOD-Scores
## 79 --> CA315 : ...................
## 383 --> MgSTS419 : ...................
## 304 --> MgSTS68 : ...................
##
##
## Placing remaining marker(s) at most likely position
## 304 --> MgSTS68 : ...................
## 79 --> CA315 : ....................
## 383 --> MgSTS419 : .....................
##
## Estimating final genetic map using tol = 10E-5.LG10_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 117 CB172 0.00
## 35 BA334 24.42
## 390 MgSTS577 29.92
## 284 MgSTS45 30.84
## 285 MgSTS11 32.08
## 407 MgSTS104 42.30
## 416 MgSTS599 53.45
## 123 CB55 58.31
## 164 CB263C 84.68
## 281 MgSTS55 99.67
## 121 CB126 114.91
## 170 AAT240 120.68
## 410 MgSTS622 129.22
## 330 MgSTS326 140.18
## 48 BA145 147.62
## 241 CC150 160.64
## 207 BC199 175.46
## 63 BB198 186.05
##
## 18 markers log-likelihood: -2211.618
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------
## | | 79 | 383 | 304 |
## |-----|-----|-----|-----|
## | | | | |
## | 117 | | | |
## | | | | |
## | 35 | | | |
## | | | | |
## | 390 | | | |
## | | | | |
## | 284 | | | |
## | | | | |
## | 285 | | | |
## | | | | |
## | 407 | | | |
## | | | | |
## | 416 | | | |
## | | | | |
## | 123 | | | |
## | | *** | | |
## | 164 | | | |
## | | * | | |
## | 281 | | | |
## | | | | |
## | 121 | | | |
## | | | | |
## | 170 | | | |
## | | | | |
## | 410 | | | |
## | | | | |
## | 330 | | | |
## | | | | |
## | 48 | | | |
## | | | | |
## | 241 | | | |
## | | | | |
## | 207 | | | |
## | | | *** | *** |
## | 63 | | | |
## | | | ** | |
## -------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_10 <- make_seq(LG10_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 117 CB172 0.00
## 35 BA334 24.42
## 390 MgSTS577 29.92
## 284 MgSTS45 30.84
## 285 MgSTS11 32.08
## 407 MgSTS104 42.29
## 416 MgSTS599 53.40
## 123 CB55 58.35
## 79 CA315 81.83
## 164 CB263C 87.98
## 281 MgSTS55 103.01
## 121 CB126 118.28
## 170 AAT240 124.06
## 410 MgSTS622 132.60
## 330 MgSTS326 143.61
## 48 BA145 149.46
## 241 CC150 159.60
## 207 BC199 170.66
## 304 MgSTS68 178.82
## 383 MgSTS419 179.82
## 63 BB198 188.68
##
## 21 markers log-likelihood: -2461.676#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
HGL13<-rf_graph_table(Ligação_grupo_10, axis.cex=.6, inter=FALSE)
GL13<-Ligação_grupo_10ORDERING MARKERS THE NEXT LINKAGE GROUP
set_map_fun(type = c("kosambi"))
LG1_f2 <- make_seq(LGs_f2, 1)
LG1_f2##
## Number of markers: 82
## Too many markers - not printing their names
##
## Parameters not estimated.LG1_rcd_f2 <- rcd(LG1_f2)##
## order obtained using RCD algorithm:
##
## 167 1 226 8 33 169 163 132 243 220 16 328 47 41 49 258 97 28 190 177 325 307 379 261 353 85 394 335 346 60 134 105 350 362 385 262 334 279 275 361 21 260 377 308 216 236 370 396 266 259 100 199 337 288 286 287 339 380 147 43 69 128 251 320 355 406 265 31 26 219 250 278 270 404 338 277 263 127 249 283 290 276
##
## calculating multipoint map using tol = 1e-04 .LG1_f2_ord <- order_seq(input.seq = LG1_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 167 1 226 8 33 169 163 132 243 220 16 328 47 41 49 258 97 28 190 177 325 307 379 261 353 85 394 335 346 60 134 105 350 362 385 262 334 279 275 361 21 260 377 308 216 236 370 396 266 259 100 199 337 288 286 287 339 380 147 43 69 128 251 320 355 406 265 31 26 219 250 278 270 404 338 277 263 127 249 283 290 276
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 394 --> MgSTS494 : ......
## 396 --> MgSTS483 : .......
## 163 --> CA389C : ........
## 385 --> MgSTS632 : ........
## 16 --> AA173C : .........
## 370 --> MgSTS583 : .........
## 377 --> MgSTS631 : .........
## 279 --> MgSTS133 : ..........
## 169 --> AAT267 : ...........
## 177 --> AAT265 : ...........
## 277 --> MgSTS91 : ...........
## 380 --> MgSTS561 : ...........
## 270 --> MgSTS26 : ...........
## 278 --> MgSTS93 : ...........
## 263 --> MgSTS20 : ...........
## 406 --> MgSTS620 : ...........
## 379 --> MgSTS562 : ...........
## 262 --> MgSTS18 : ............
## 307 --> MgSTS527 : .............
## 288 --> MgSTS87 : ..............
## 283 --> MgSTS98 : ..............
## 266 --> MgSTS24 : ..............
## 265 --> MgSTS19 : ..............
## 308 --> MgSTS520 : ..............
## 337 --> MgSTS358 : ...............
## 335 --> MgSTS348 : ...............
## 220 --> BC194C : ................
## 219 --> BC526C : ................
## 338 --> MgSTS344 : ................
## 334 --> MgSTS350 : ................
## 404 --> MgSTS598 : .................
## 290 --> MgSTS212 : .................
## 320 --> MgSTS360 : .................
## 362 --> MgSTS578 : .................
## 355 --> MgSTS380 : ..................
## 350 --> MgSTS500 : ..................
## 287 --> aat356 : ...................
## 346 --> MgSTS491 : ...................
## 261 --> MgSTS16 : ...................
## 275 --> MgSTS29 : ....................
## 259 --> AP3 : .....................
## 286 --> CYCA : .....................
## 353 --> MgSTS398 : .....................
## 361 --> MgSTS263 : .....................
## 339 --> MgSTS471 : .....................
## 258 --> AAT333 : .....................
## 328 --> MgSTS336 : .....................
## 69 --> BB124 : .....................
## 97 --> CA174 : .....................
## 100 --> CA150 : .....................
## 1 --> AA461 : ......................
## 49 --> BA129 : ......................
## 28 --> BA416 : ......................
## 43 --> BA196 : ......................
## 31 --> BA387 : ......................
## 26 --> BA449 : ......................
## 134 --> BD251 : ......................
## 147 --> BD100 : .......................
## 127 --> BD371 : .......................
## 216 --> BC80 : ........................
## 199 --> BC374 : ........................
## 226 --> CC447 : ........................
## 236 --> CC320 : ........................
## 251 --> CC53 : .........................
## 250 --> CC61 : .........................
## 60 --> BB216 : .........................
## 85 --> CA267 : .........................
## 105 --> CA75 : .........................
## 8 --> AA341 : ..........................
## 21 --> AA137 : ..........................
## 33 --> BA374 : ...........................
## 47 --> BA153 : ...........................
## 41 --> BA214 : ...........................
## 132 --> BD270 : ...........................
## 190 --> BC542 : ...........................
## 243 --> CC138 : ............................
## 249 --> CC93 : ............................
##
## LOD threshold = 3
##
## Positioned markers: 167 128 100 236 396 308 377 260 21 275 127 279 334 262 385 362 350 105 134 276 335 394 261 379 307 325 190
##
## Markers not placed on the map: 1 226 8 33 169 163 132 243 220 16 328 47 41 49 258 97 28 177 353 85 346 60 361 216 370 266 259 199 337 288 286 287 339 380 147 43 69 251 320 355 406 265 31 26 219 250 278 270 404 338 277 263 249 283 290
##
##
## Calculating LOD-Scores
## 1 --> AA461 : ............................
## 226 --> CC447 : ............................
## 8 --> AA341 : ............................
## 33 --> BA374 : ............................
## 169 --> AAT267 : ............................
## 163 --> CA389C : ............................
## 132 --> BD270 : ............................
## 243 --> CC138 : ............................
## 220 --> BC194C : ............................
## 16 --> AA173C : ............................
## 328 --> MgSTS336 : ............................
## 47 --> BA153 : ............................
## 41 --> BA214 : ............................
## 49 --> BA129 : ............................
## 258 --> AAT333 : ............................
## 97 --> CA174 : ............................
## 28 --> BA416 : ............................
## 177 --> AAT265 : ............................
## 353 --> MgSTS398 : ............................
## 85 --> CA267 : ............................
## 346 --> MgSTS491 : ............................
## 60 --> BB216 : ............................
## 361 --> MgSTS263 : ............................
## 216 --> BC80 : ............................
## 370 --> MgSTS583 : ............................
## 266 --> MgSTS24 : ............................
## 259 --> AP3 : ............................
## 199 --> BC374 : ............................
## 337 --> MgSTS358 : ............................
## 288 --> MgSTS87 : ............................
## 286 --> CYCA : ............................
## 287 --> aat356 : ............................
## 339 --> MgSTS471 : ............................
## 380 --> MgSTS561 : ............................
## 147 --> BD100 : ............................
## 43 --> BA196 : ............................
## 69 --> BB124 : ............................
## 251 --> CC53 : ............................
## 320 --> MgSTS360 : ............................
## 355 --> MgSTS380 : ............................
## 406 --> MgSTS620 : ............................
## 265 --> MgSTS19 : ............................
## 31 --> BA387 : ............................
## 26 --> BA449 : ............................
## 219 --> BC526C : ............................
## 250 --> CC61 : ............................
## 278 --> MgSTS93 : ............................
## 270 --> MgSTS26 : ............................
## 404 --> MgSTS598 : ............................
## 338 --> MgSTS344 : ............................
## 277 --> MgSTS91 : ............................
## 263 --> MgSTS20 : ............................
## 249 --> CC93 : ............................
## 283 --> MgSTS98 : ............................
## 290 --> MgSTS212 : ............................
##
##
## Placing remaining marker(s) at most likely position
## 266 --> MgSTS24 : ............................
## 177 --> AAT265 : .............................
## 370 --> MgSTS583 : ..............................
## 216 --> BC80 : ...............................
## 169 --> AAT267 : ................................
## 355 --> MgSTS380 : .................................
## 250 --> CC61 : ..................................
## 288 --> MgSTS87 : ...................................
## 219 --> BC526C : ....................................
## 270 --> MgSTS26 : .....................................
## 353 --> MgSTS398 : ......................................
## 380 --> MgSTS561 : .......................................
## 278 --> MgSTS93 : ........................................
## 26 --> BA449 : .........................................
## 404 --> MgSTS598 : ..........................................
## 346 --> MgSTS491 : ...........................................
## 199 --> BC374 : ............................................
## 31 --> BA387 : .............................................
## 338 --> MgSTS344 : ..............................................
## 259 --> AP3 : ...............................................
## 286 --> CYCA : ................................................
## 163 --> CA389C : .................................................
## 28 --> BA416 : ..................................................
## 263 --> MgSTS20 : ...................................................
## 361 --> MgSTS263 : ....................................................
## 265 --> MgSTS19 : .....................................................
## 132 --> BD270 : ......................................................
## 220 --> BC194C : .......................................................
## 290 --> MgSTS212 : ........................................................
## 243 --> CC138 : .........................................................
## 283 --> MgSTS98 : ..........................................................
## 277 --> MgSTS91 : ...........................................................
## 258 --> AAT333 : ............................................................
## 287 --> aat356 : .............................................................
## 47 --> BA153 : ..............................................................
## 16 --> AA173C : ...............................................................
## 8 --> AA341 : ................................................................
## 85 --> CA267 : .................................................................
## 339 --> MgSTS471 : ..................................................................
## 328 --> MgSTS336 : ...................................................................
## 60 --> BB216 : ....................................................................
## 97 --> CA174 : .....................................................................
## 1 --> AA461 : ......................................................................
## 406 --> MgSTS620 : .......................................................................
## 251 --> CC53 : ........................................................................
## 33 --> BA374 : .........................................................................
## 41 --> BA214 : ..........................................................................
## 147 --> BD100 : ...........................................................................
## 43 --> BA196 : ............................................................................
## 249 --> CC93 : .............................................................................
## 226 --> CC447 : ..............................................................................
## 49 --> BA129 : ...............................................................................
## 69 --> BB124 : ................................................................................
## 337 --> MgSTS358 : .................................................................................
## 320 --> MgSTS360 : ..................................................................................
##
## Estimating final genetic map using tol = 10E-5.LG1_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 167 AAT225 0.00
## 128 BD340 65.75
## 100 CA150 111.49
## 236 CC320 121.51
## 396 MgSTS483 130.51
## 308 MgSTS520 160.49
## 377 MgSTS631 166.19
## 260 MgSTS17 171.68
## 21 AA137 175.45
## 275 MgSTS29 182.37
## 127 BD371 188.49
## 279 MgSTS133 194.56
## 334 MgSTS350 202.23
## 262 MgSTS18 214.63
## 385 MgSTS632 220.00
## 362 MgSTS578 227.95
## 350 MgSTS500 231.82
## 105 CA75 234.47
## 134 BD251 244.43
## 276 MgSTS38 278.37
## 335 MgSTS348 315.88
## 394 MgSTS494 336.61
## 261 MgSTS16 352.02
## 379 MgSTS562 359.59
## 307 MgSTS527 363.89
## 325 MgSTS341 369.27
## 190 BC542 381.66
##
## 27 markers log-likelihood: -3760.981
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
## | | 1 | 226 | 8 | 33 | 169 | 163 | 132 | 243 | 220 | 16 | 328 | 47 | 41 | 49 | 258 | 97 | 28 | 177 | 353 | 85 | 346 | 60 | 361 | 216 | 370 | 266 | 259 | 199 | 337 | 288 | 286 | 287 | 339 | 380 | 147 | 43 | 69 | 251 | 320 | 355 | 406 | 265 | 31 | 26 | 219 | 250 | 278 | 270 | 404 | 338 | 277 | 263 | 249 | 283 | 290 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | ** | ** | ** | ** | | * | *** | *** | *** | *** | *** | *** | ** | ** | *** | ** | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * | * | | | | *** | *** |
## | 167 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | *** | *** | *** | *** | *** | *** | ** | ** | ** | ** | ** | ** | *** | *** | ** | *** | *** | | | | | | | | | | | * | ** | *** | *** | *** | *** | *** | *** | ** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | | ** | ** |
## | 128 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | *** | *** | *** | | * | ** | ** | | ** | *** | ** | ** | ** | | ** | * | * | * | | | * | | | | ** | * | | | |
## | 100 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | *** | | | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 236 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | *** | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 396 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 308 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 377 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 260 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 21 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 275 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | *** | | |
## | 127 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ** | | |
## | 279 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 334 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 262 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 385 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 362 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 350 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 105 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | ** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 134 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 276 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 335 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | ** | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 394 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 261 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 379 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 307 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 325 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 190 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_1 <- make_seq(LG1_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 8 AA341 0.00
## 33 BA374 10.81
## 167 AAT225 25.53
## 1 AA461 49.12
## 226 CC447 57.01
## 258 AAT333 73.53
## 97 CA174 81.98
## 28 BA416 90.20
## 163 CA389C 100.50
## 49 BA129 108.00
## 169 AAT267 119.66
## 41 BA214 129.65
## 132 BD270 141.59
## 16 AA173C 157.32
## 328 MgSTS336 165.15
## 47 BA153 170.61
## 243 CC138 180.74
## 220 BC194C 193.44
## 283 MgSTS98 214.14
## 290 MgSTS212 219.88
## 355 MgSTS380 622.83
## 320 MgSTS360 629.77
## 251 CC53 638.52
## 128 BD340 643.47
## 147 BD100 649.89
## 288 MgSTS87 656.36
## 287 aat356 658.26
## 286 CYCA 658.26
## 339 MgSTS471 659.55
## 380 MgSTS561 661.42
## 69 BB124 668.33
## 43 BA196 668.33
## 337 MgSTS358 682.95
## 199 BC374 710.64
## 406 MgSTS620 748.00
## 265 MgSTS19 755.88
## 31 BA387 765.05
## 263 MgSTS20 777.09
## 277 MgSTS91 780.36
## 26 BA449 784.81
## 219 BC526C 786.72
## 250 CC61 790.70
## 278 MgSTS93 797.12
## 270 MgSTS26 798.30
## 404 MgSTS598 802.68
## 338 MgSTS344 805.09
## 259 AP3 888.23
## 100 CA150 891.53
## 216 BC80 899.71
## 236 CC320 905.70
## 370 MgSTS583 909.68
## 266 MgSTS24 914.74
## 396 MgSTS483 919.66
## 308 MgSTS520 949.83
## 377 MgSTS631 955.53
## 260 MgSTS17 960.91
## 21 AA137 964.70
## 275 MgSTS29 971.81
## 361 MgSTS263 974.32
## 127 BD371 982.16
## 249 CC93 982.16
## 279 MgSTS133 990.56
## 334 MgSTS350 998.23
## 262 MgSTS18 1010.78
## 385 MgSTS632 1016.18
## 362 MgSTS578 1024.13
## 350 MgSTS500 1028.07
## 105 CA75 1030.57
## 134 BD251 1041.73
## 60 BB216 1048.37
## 276 MgSTS38 1076.75
## 346 MgSTS491 1108.02
## 335 MgSTS348 1112.12
## 85 CA267 1135.84
## 394 MgSTS494 1143.97
## 261 MgSTS16 1159.06
## 353 MgSTS398 1162.43
## 379 MgSTS562 1167.22
## 307 MgSTS527 1171.46
## 325 MgSTS341 1176.68
## 177 AAT265 1185.52
## 190 BC542 1201.30
##
## 82 markers log-likelihood: -9401.224#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_1, axis.cex=.6, inter=FALSE)
Ligação_grupo_1##
## Printing map:
##
## Markers Position
##
## 8 AA341 0.00
## 33 BA374 10.81
## 167 AAT225 25.53
## 1 AA461 49.12
## 226 CC447 57.01
## 258 AAT333 73.53
## 97 CA174 81.98
## 28 BA416 90.20
## 163 CA389C 100.50
## 49 BA129 108.00
## 169 AAT267 119.66
## 41 BA214 129.65
## 132 BD270 141.59
## 16 AA173C 157.32
## 328 MgSTS336 165.15
## 47 BA153 170.61
## 243 CC138 180.74
## 220 BC194C 193.44
## 283 MgSTS98 214.14
## 290 MgSTS212 219.88
## 355 MgSTS380 622.83
## 320 MgSTS360 629.77
## 251 CC53 638.52
## 128 BD340 643.47
## 147 BD100 649.89
## 288 MgSTS87 656.36
## 287 aat356 658.26
## 286 CYCA 658.26
## 339 MgSTS471 659.55
## 380 MgSTS561 661.42
## 69 BB124 668.33
## 43 BA196 668.33
## 337 MgSTS358 682.95
## 199 BC374 710.64
## 406 MgSTS620 748.00
## 265 MgSTS19 755.88
## 31 BA387 765.05
## 263 MgSTS20 777.09
## 277 MgSTS91 780.36
## 26 BA449 784.81
## 219 BC526C 786.72
## 250 CC61 790.70
## 278 MgSTS93 797.12
## 270 MgSTS26 798.30
## 404 MgSTS598 802.68
## 338 MgSTS344 805.09
## 259 AP3 888.23
## 100 CA150 891.53
## 216 BC80 899.71
## 236 CC320 905.70
## 370 MgSTS583 909.68
## 266 MgSTS24 914.74
## 396 MgSTS483 919.66
## 308 MgSTS520 949.83
## 377 MgSTS631 955.53
## 260 MgSTS17 960.91
## 21 AA137 964.70
## 275 MgSTS29 971.81
## 361 MgSTS263 974.32
## 127 BD371 982.16
## 249 CC93 982.16
## 279 MgSTS133 990.56
## 334 MgSTS350 998.23
## 262 MgSTS18 1010.78
## 385 MgSTS632 1016.18
## 362 MgSTS578 1024.13
## 350 MgSTS500 1028.07
## 105 CA75 1030.57
## 134 BD251 1041.73
## 60 BB216 1048.37
## 276 MgSTS38 1076.75
## 346 MgSTS491 1108.02
## 335 MgSTS348 1112.12
## 85 CA267 1135.84
## 394 MgSTS494 1143.97
## 261 MgSTS16 1159.06
## 353 MgSTS398 1162.43
## 379 MgSTS562 1167.22
## 307 MgSTS527 1171.46
## 325 MgSTS341 1176.68
## 177 AAT265 1185.52
## 190 BC542 1201.30
##
## 82 markers log-likelihood: -9401.224We are going to create subgroups of the group 1
set_map_fun(type = c("kosambi"))
GL1_inicial <- group(LG1_f2, LOD=6, max.rf=0.25)## Selecting markers:
## group 1
## ....................
## group 2
## ...................................
## group 3
## ..........................GL1_inicial## This is an object of class 'group'
## It was generated from the object "LG1_f2"
##
## Criteria used to assign markers to groups:
## LOD = 6 , Maximum recombination fraction = 0.25
##
## No. markers: 82
## No. groups: 3
## No. linked markers: 81
## No. unlinked markers: 1
##
## Printing groups:
## Group 1 : 20 markers
## AA461 AA341 AA173C BA416 BA374 BA214 BA153 BA129 CA174 BD270 CA389C AAT225 AAT267 BC194C CC447 CC138 AAT333 MgSTS98 MgSTS212 MgSTS336
##
## Group 2 : 35 markers
## AA137 BB216 CA267 CA150 CA75 BD371 BD251 AAT265 BC542 BC80 CC320 CC93 AP3 MgSTS17 MgSTS16 MgSTS18 MgSTS24 MgSTS29 MgSTS133 MgSTS527 MgSTS520 MgSTS341 MgSTS350 MgSTS348 MgSTS491 MgSTS500 MgSTS398 MgSTS263 MgSTS578 MgSTS583 MgSTS631 MgSTS562 MgSTS632 MgSTS494 MgSTS483
##
## Group 3 : 26 markers
## BA449 BA387 BA196 BB124 BD340 BD100 BC374 BC526C CC61 CC53 MgSTS20 MgSTS19 MgSTS26 MgSTS91 MgSTS93 CYCA aat356 MgSTS87 MgSTS360 MgSTS358 MgSTS344 MgSTS471 MgSTS380 MgSTS561 MgSTS598 MgSTS620
##
## Unlinked markers: 1 markers
## MgSTS38GL1_1<-make_seq(GL1_inicial, 1)Ordering markers within subgroup 1 of the group 1
LG1_1_f2 <- rcd(GL1_1)##
## order obtained using RCD algorithm:
##
## 167 8 33 1 226 258 28 97 163 49 41 47 328 16 220 243 132 169 283 290
##
## calculating multipoint map using tol = 1e-04 .LG1_1_f2##
## Printing map:
##
## Markers Position
##
## 167 AAT225 0.00
## 8 AA341 20.69
## 33 BA374 30.89
## 1 AA461 39.21
## 226 CC447 47.31
## 258 AAT333 64.30
## 28 BA416 73.80
## 97 CA174 81.83
## 163 CA389C 91.32
## 49 BA129 100.95
## 41 BA214 106.12
## 47 BA153 118.64
## 328 MgSTS336 125.63
## 16 AA173C 133.72
## 220 BC194C 150.60
## 243 CC138 166.72
## 132 BD270 191.48
## 169 AAT267 214.64
## 283 MgSTS98 267.13
## 290 MgSTS212 272.98
##
## 20 markers log-likelihood: -2757.054LG1_1_f2_ord <- order_seq(input.seq = LG1_1_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 167 8 33 1 226 258 28 97 163 49 41 47 328 16 220 243 132 169 283 290
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
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##
##
##
## Running try algorithm
## 163 --> CA389C : ......
## 16 --> AA173C : .......
## 169 --> AAT267 : ........
## 283 --> MgSTS98 : .........
## 328 --> MgSTS336 : ..........
## 97 --> CA174 : ...........
## 1 --> AA461 : ............
## 28 --> BA416 : .............
## 226 --> CC447 : ..............
## 8 --> AA341 : ..............
## 33 --> BA374 : ...............
## 41 --> BA214 : ................
## 47 --> BA153 : .................
## 132 --> BD270 : .................
## 243 --> CC138 : ..................
##
## LOD threshold = 3
##
## Positioned markers: 8 33 167 1 28 258 97 163 49 169 41 132 16 328 243 220 283 290
##
## Markers not placed on the map: 226 47
##
##
## Calculating LOD-Scores
## 226 --> CC447 : ...................
## 47 --> BA153 : ...................
##
##
## Placing remaining marker(s) at most likely position
## 226 --> CC447 : ...................
## 47 --> BA153 : ....................
##
## Estimating final genetic map using tol = 10E-5.LG1_1_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 8 AA341 0.00
## 33 BA374 10.81
## 167 AAT225 25.49
## 1 AA461 48.93
## 28 BA416 62.52
## 258 AAT333 70.72
## 97 CA174 79.01
## 163 CA389C 90.33
## 49 BA129 97.87
## 169 AAT267 109.53
## 41 BA214 119.52
## 132 BD270 131.47
## 16 AA173C 147.20
## 328 MgSTS336 155.96
## 243 CC138 166.17
## 220 BC194C 179.05
## 283 MgSTS98 199.55
## 290 MgSTS212 205.24
##
## 18 markers log-likelihood: -2456.461
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------
## | | 226 | 47 |
## |-----|-----|-----|
## | | | |
## | 8 | | |
## | | | |
## | 33 | | |
## | | | |
## | 167 | | |
## | | ** | |
## | 1 | | |
## | | *** | |
## | 28 | | |
## | | | |
## | 258 | | |
## | | | |
## | 97 | | |
## | | | |
## | 163 | | |
## | | | |
## | 49 | | |
## | | | |
## | 169 | | |
## | | | |
## | 41 | | |
## | | | |
## | 132 | | |
## | | | |
## | 16 | | |
## | | | ** |
## | 328 | | |
## | | | *** |
## | 243 | | |
## | | | |
## | 220 | | |
## | | | |
## | 283 | | |
## | | | |
## | 290 | | |
## | | | |
## -------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_1_1 <- make_seq(LG1_1_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 8 AA341 0.00
## 33 BA374 10.81
## 167 AAT225 25.49
## 1 AA461 48.96
## 226 CC447 56.72
## 28 BA416 69.73
## 258 AAT333 77.78
## 97 CA174 86.07
## 163 CA389C 97.39
## 49 BA129 104.93
## 169 AAT267 116.59
## 41 BA214 126.58
## 132 BD270 138.52
## 16 AA173C 154.26
## 328 MgSTS336 162.08
## 47 BA153 167.54
## 243 CC138 177.67
## 220 BC194C 190.37
## 283 MgSTS98 211.07
## 290 MgSTS212 216.81
##
## 20 markers log-likelihood: -2588.519#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_1_1, axis.cex=.6, inter=FALSE)
Ligação_grupo_1_1##
## Printing map:
##
## Markers Position
##
## 8 AA341 0.00
## 33 BA374 10.81
## 167 AAT225 25.49
## 1 AA461 48.96
## 226 CC447 56.72
## 28 BA416 69.73
## 258 AAT333 77.78
## 97 CA174 86.07
## 163 CA389C 97.39
## 49 BA129 104.93
## 169 AAT267 116.59
## 41 BA214 126.58
## 132 BD270 138.52
## 16 AA173C 154.26
## 328 MgSTS336 162.08
## 47 BA153 167.54
## 243 CC138 177.67
## 220 BC194C 190.37
## 283 MgSTS98 211.07
## 290 MgSTS212 216.81
##
## 20 markers log-likelihood: -2588.519LG1_1_seq_f2_rm <- drop_marker(Ligação_grupo_1_1, c(226, 47))
LG1_1_rcd_f2_rm <- rcd(LG1_1_seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 167 8 33 1 258 28 97 163 49 41 169 16 328 220 243 132 283 290
##
## calculating multipoint map using tol = 1e-04 .LG1_1_rcd_f2_rm##
## Printing map:
##
## Markers Position
##
## 167 AAT225 0.00
## 8 AA341 20.37
## 33 BA374 30.42
## 1 AA461 39.98
## 258 AAT333 60.44
## 28 BA416 69.21
## 97 CA174 77.33
## 163 CA389C 86.90
## 49 BA129 96.53
## 41 BA214 101.04
## 169 AAT267 112.39
## 16 AA173C 131.76
## 328 MgSTS336 140.10
## 220 BC194C 153.56
## 243 CC138 169.21
## 132 BD270 190.78
## 283 MgSTS98 226.33
## 290 MgSTS212 232.22
##
## 18 markers log-likelihood: -2548.701LG1_1_f2_ord_rm <- order_seq(input.seq = LG1_1_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 167 8 33 1 258 28 97 163 49 41 169 16 328 220 243 132 283 290
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
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##
##
##
## Running try algorithm
## 163 --> CA389C : ......
## 16 --> AA173C : .......
## 169 --> AAT267 : ........
## 283 --> MgSTS98 : .........
## 328 --> MgSTS336 : ..........
## 97 --> CA174 : ...........
## 1 --> AA461 : ............
## 28 --> BA416 : .............
## 49 --> BA129 : ..............
## 8 --> AA341 : ...............
## 33 --> BA374 : ................
## 132 --> BD270 : .................
## 243 --> CC138 : ..................
##
## LOD threshold = 3
##
## Positioned markers: 8 33 167 1 28 258 97 163 49 169 41 132 16 328 243 220 283 290
##
## Markers not placed on the map:
##
## Estimating final genetic map using tol = 10E-5.LG1_1_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 8 AA341 0.00
## 33 BA374 10.81
## 167 AAT225 25.49
## 1 AA461 48.93
## 28 BA416 62.52
## 258 AAT333 70.72
## 97 CA174 79.01
## 163 CA389C 90.33
## 49 BA129 97.87
## 169 AAT267 109.53
## 41 BA214 119.52
## 132 BD270 131.47
## 16 AA173C 147.20
## 328 MgSTS336 155.96
## 243 CC138 166.17
## 220 BC194C 179.05
## 283 MgSTS98 199.55
## 290 MgSTS212 205.24
##
## 18 markers log-likelihood: -2456.461(Ligação_grupo_1_1rm <- make_seq(LG1_1_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 8 AA341 0.00
## 33 BA374 10.81
## 167 AAT225 25.49
## 1 AA461 48.93
## 28 BA416 62.52
## 258 AAT333 70.72
## 97 CA174 79.01
## 163 CA389C 90.33
## 49 BA129 97.87
## 169 AAT267 109.53
## 41 BA214 119.52
## 132 BD270 131.47
## 16 AA173C 147.20
## 328 MgSTS336 155.96
## 243 CC138 166.17
## 220 BC194C 179.05
## 283 MgSTS98 199.55
## 290 MgSTS212 205.24
##
## 18 markers log-likelihood: -2456.461HGL1<-rf_graph_table(Ligação_grupo_1_1rm, axis.cex=.6, inter=FALSE)
GL1<-Ligação_grupo_1_1rmThe same step for subgroup 2 of the group 1
GL1_2<-make_seq(GL1_inicial, 2)
GL1_2##
## Number of markers: 35
## Markers in the sequence:
## AA137 BB216 CA267 CA150 CA75 BD371 BD251 AAT265 BC542 BC80 CC320 CC93 AP3
## MgSTS17 MgSTS16 MgSTS18 MgSTS24 MgSTS29 MgSTS133 MgSTS527 MgSTS520
## MgSTS341 MgSTS350 MgSTS348 MgSTS491 MgSTS500 MgSTS398 MgSTS263 MgSTS578
## MgSTS583 MgSTS631 MgSTS562 MgSTS632 MgSTS494 MgSTS483
##
## Parameters not estimated.LG1_2_f2 <- rcd(GL1_2)##
## order obtained using RCD algorithm:
##
## 216 100 259 396 266 236 370 308 377 21 260 127 249 275 361 279 334 262 385 362 350 105 134 60 346 335 394 85 353 261 379 307 325 177 190
##
## calculating multipoint map using tol = 1e-04 .LG1_2_f2##
## Printing map:
##
## Markers Position
##
## 216 BC80 0.00
## 100 CA150 10.48
## 259 AP3 14.44
## 396 MgSTS483 24.74
## 266 MgSTS24 29.65
## 236 CC320 34.75
## 370 MgSTS583 38.65
## 308 MgSTS520 63.04
## 377 MgSTS631 68.84
## 21 AA137 74.57
## 260 MgSTS17 78.40
## 127 BD371 91.57
## 249 CC93 91.84
## 275 MgSTS29 99.38
## 361 MgSTS263 102.07
## 279 MgSTS133 106.70
## 334 MgSTS350 114.64
## 262 MgSTS18 127.19
## 385 MgSTS632 132.56
## 362 MgSTS578 140.51
## 350 MgSTS500 144.50
## 105 CA75 146.79
## 134 BD251 161.07
## 60 BB216 161.77
## 346 MgSTS491 178.86
## 335 MgSTS348 182.79
## 394 MgSTS494 203.68
## 85 CA267 210.85
## 353 MgSTS398 224.14
## 261 MgSTS16 227.32
## 379 MgSTS562 234.67
## 307 MgSTS527 238.93
## 325 MgSTS341 244.15
## 177 AAT265 252.98
## 190 BC542 268.75
##
## 35 markers log-likelihood: -3997.561LG1_2_f2_ord <- order_seq(input.seq = LG1_2_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 216 100 259 396 266 236 370 308 377 21 260 127 249 275 361 279 334 262 385 362 350 105 134 60 346 335 394 85 353 261 379 307 325 177 190
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 394 --> MgSTS494 : ......
## 396 --> MgSTS483 : .......
## 385 --> MgSTS632 : .......
## 370 --> MgSTS583 : ........
## 377 --> MgSTS631 : ........
## 279 --> MgSTS133 : ........
## 177 --> AAT265 : .........
## 260 --> MgSTS17 : ..........
## 379 --> MgSTS562 : ...........
## 307 --> MgSTS527 : ............
## 266 --> MgSTS24 : .............
## 308 --> MgSTS520 : .............
## 334 --> MgSTS350 : ..............
## 362 --> MgSTS578 : ...............
## 350 --> MgSTS500 : ................
## 346 --> MgSTS491 : .................
## 261 --> MgSTS16 : .................
## 275 --> MgSTS29 : ..................
## 259 --> AP3 : ...................
## 353 --> MgSTS398 : ...................
## 361 --> MgSTS263 : ...................
## 325 --> MgSTS341 : ...................
## 100 --> CA150 : ....................
## 127 --> BD371 : ....................
## 134 --> BD251 : .....................
## 236 --> CC320 : ......................
## 60 --> BB216 : ......................
## 105 --> CA75 : ......................
## 85 --> CA267 : .......................
## 249 --> CC93 : .......................
##
## LOD threshold = 3
##
## Positioned markers: 216 308 21 260 275 127 279 334 262 385 362 350 105 134 335 394 261 379 307 325 177 190
##
## Markers not placed on the map: 100 259 396 266 236 370 377 249 361 60 346 85 353
##
##
## Calculating LOD-Scores
## 100 --> CA150 : .......................
## 259 --> AP3 : .......................
## 396 --> MgSTS483 : .......................
## 266 --> MgSTS24 : .......................
## 236 --> CC320 : .......................
## 370 --> MgSTS583 : .......................
## 377 --> MgSTS631 : .......................
## 249 --> CC93 : .......................
## 361 --> MgSTS263 : .......................
## 60 --> BB216 : .......................
## 346 --> MgSTS491 : .......................
## 85 --> CA267 : .......................
## 353 --> MgSTS398 : .......................
##
##
## Placing remaining marker(s) at most likely position
## 370 --> MgSTS583 : .......................
## 377 --> MgSTS631 : ........................
## 396 --> MgSTS483 : .........................
## 266 --> MgSTS24 : ..........................
## 236 --> CC320 : ...........................
## 353 --> MgSTS398 : ............................
## 361 --> MgSTS263 : .............................
## 346 --> MgSTS491 : ..............................
## 85 --> CA267 : ...............................
## 100 --> CA150 : ................................
## 249 --> CC93 : .................................
## 60 --> BB216 : ..................................
## 259 --> AP3 : ...................................
##
## Estimating final genetic map using tol = 10E-5.LG1_2_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 216 BC80 0.00
## 308 MgSTS520 35.19
## 21 AA137 44.01
## 260 MgSTS17 48.64
## 275 MgSTS29 56.59
## 127 BD371 62.45
## 279 MgSTS133 68.27
## 334 MgSTS350 75.92
## 262 MgSTS18 88.33
## 385 MgSTS632 93.70
## 362 MgSTS578 101.64
## 350 MgSTS500 105.57
## 105 CA75 108.17
## 134 BD251 118.31
## 335 MgSTS348 134.42
## 394 MgSTS494 154.93
## 261 MgSTS16 170.27
## 379 MgSTS562 177.80
## 307 MgSTS527 182.06
## 325 MgSTS341 187.28
## 177 AAT265 196.10
## 190 BC542 211.78
##
## 22 markers log-likelihood: -2821.321
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------
## | | 100 | 259 | 396 | 266 | 236 | 370 | 377 | 249 | 361 | 60 | 346 | 85 | 353 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | *** | *** | | | | | | | | | | | |
## | 216 | | | | | | | | | | | | | |
## | | * | ** | *** | *** | *** | *** | | | | | | | |
## | 308 | | | | | | | | | | | | | |
## | | | | | | | | *** | | | | | | |
## | 21 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 260 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 275 | | | | | | | | | | | | | |
## | | | | | | | | | *** | *** | | | | |
## | 127 | | | | | | | | | | | | | |
## | | | | | | | | | ** | | | | | |
## | 279 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 334 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 262 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 385 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 362 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 350 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 105 | | | | | | | | | | | | | |
## | | | | | | | | | | | ** | | | |
## | 134 | | | | | | | | | | | | | |
## | | | | | | | | | | | *** | *** | | |
## | 335 | | | | | | | | | | | | | |
## | | | | | | | | | | | | * | * | |
## | 394 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | *** | |
## | 261 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | *** |
## | 379 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 307 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 325 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 177 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## | 190 | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | |
## -------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_1_2 <- make_seq(LG1_2_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 259 AP3 0.00
## 100 CA150 3.12
## 216 BC80 10.80
## 266 MgSTS24 15.17
## 396 MgSTS483 20.12
## 370 MgSTS583 27.92
## 236 CC320 32.16
## 308 MgSTS520 57.49
## 377 MgSTS631 63.28
## 21 AA137 68.99
## 260 MgSTS17 72.76
## 275 MgSTS29 81.35
## 361 MgSTS263 83.84
## 127 BD371 91.53
## 249 CC93 91.53
## 279 MgSTS133 99.93
## 334 MgSTS350 107.60
## 262 MgSTS18 120.16
## 385 MgSTS632 125.56
## 362 MgSTS578 133.51
## 350 MgSTS500 137.50
## 105 CA75 139.79
## 134 BD251 154.06
## 60 BB216 154.77
## 346 MgSTS491 171.85
## 335 MgSTS348 175.78
## 394 MgSTS494 196.66
## 85 CA267 204.52
## 261 MgSTS16 220.36
## 353 MgSTS398 223.72
## 379 MgSTS562 228.60
## 307 MgSTS527 232.84
## 325 MgSTS341 238.07
## 177 AAT265 246.91
## 190 BC542 262.69
##
## 35 markers log-likelihood: -3970.403#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_1_2, axis.cex=.6, inter=FALSE)
Ligação_grupo_1_2##
## Printing map:
##
## Markers Position
##
## 259 AP3 0.00
## 100 CA150 3.12
## 216 BC80 10.80
## 266 MgSTS24 15.17
## 396 MgSTS483 20.12
## 370 MgSTS583 27.92
## 236 CC320 32.16
## 308 MgSTS520 57.49
## 377 MgSTS631 63.28
## 21 AA137 68.99
## 260 MgSTS17 72.76
## 275 MgSTS29 81.35
## 361 MgSTS263 83.84
## 127 BD371 91.53
## 249 CC93 91.53
## 279 MgSTS133 99.93
## 334 MgSTS350 107.60
## 262 MgSTS18 120.16
## 385 MgSTS632 125.56
## 362 MgSTS578 133.51
## 350 MgSTS500 137.50
## 105 CA75 139.79
## 134 BD251 154.06
## 60 BB216 154.77
## 346 MgSTS491 171.85
## 335 MgSTS348 175.78
## 394 MgSTS494 196.66
## 85 CA267 204.52
## 261 MgSTS16 220.36
## 353 MgSTS398 223.72
## 379 MgSTS562 228.60
## 307 MgSTS527 232.84
## 325 MgSTS341 238.07
## 177 AAT265 246.91
## 190 BC542 262.69
##
## 35 markers log-likelihood: -3970.403LG1_2_seq_f2_rm <- drop_marker(Ligação_grupo_1_2, c(216, 335))
LG1_2_rcd_f2_rm <- rcd(LG1_2_seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 100 259 396 266 236 370 308 377 21 260 127 249 275 361 279 334 262 385 362 350 105 134 60 346 394 85 353 261 379 307 325 177 190
##
## calculating multipoint map using tol = 1e-04 .LG1_2_rcd_f2_rm##
## Printing map:
##
## Markers Position
##
## 100 CA150 0.00
## 259 AP3 3.94
## 396 MgSTS483 14.37
## 266 MgSTS24 19.28
## 236 CC320 24.38
## 370 MgSTS583 28.28
## 308 MgSTS520 52.67
## 377 MgSTS631 58.47
## 21 AA137 64.19
## 260 MgSTS17 68.03
## 127 BD371 81.19
## 249 CC93 81.47
## 275 MgSTS29 89.01
## 361 MgSTS263 91.70
## 279 MgSTS133 96.33
## 334 MgSTS350 104.27
## 262 MgSTS18 116.82
## 385 MgSTS632 122.19
## 362 MgSTS578 130.14
## 350 MgSTS500 134.13
## 105 CA75 136.44
## 134 BD251 150.22
## 60 BB216 151.80
## 346 MgSTS491 168.72
## 394 MgSTS494 187.63
## 85 CA267 194.82
## 353 MgSTS398 208.10
## 261 MgSTS16 211.29
## 379 MgSTS562 218.64
## 307 MgSTS527 222.90
## 325 MgSTS341 228.12
## 177 AAT265 236.95
## 190 BC542 252.72
##
## 33 markers log-likelihood: -3813.882LG1_2_f2_ord_rm <- order_seq(input.seq = LG1_2_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 100 259 396 266 236 370 308 377 21 260 127 249 275 361 279 334 262 385 362 350 105 134 60 346 394 85 353 261 379 307 325 177 190
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
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##
##
##
## Running try algorithm
## 396 --> MgSTS483 : ......
## 385 --> MgSTS632 : ......
## 370 --> MgSTS583 : ......
## 377 --> MgSTS631 : ......
## 279 --> MgSTS133 : ......
## 177 --> AAT265 : .......
## 260 --> MgSTS17 : ........
## 379 --> MgSTS562 : .........
## 307 --> MgSTS527 : ..........
## 266 --> MgSTS24 : ...........
## 308 --> MgSTS520 : ...........
## 334 --> MgSTS350 : ............
## 362 --> MgSTS578 : .............
## 350 --> MgSTS500 : ..............
## 346 --> MgSTS491 : ...............
## 261 --> MgSTS16 : ................
## 275 --> MgSTS29 : .................
## 259 --> AP3 : ..................
## 353 --> MgSTS398 : ..................
## 361 --> MgSTS263 : ..................
## 325 --> MgSTS341 : ..................
## 127 --> BD371 : ...................
## 134 --> BD251 : ....................
## 236 --> CC320 : .....................
## 60 --> BB216 : ......................
## 105 --> CA75 : ......................
## 85 --> CA267 : .......................
## 249 --> CC93 : .......................
##
## LOD threshold = 3
##
## Positioned markers: 100 236 308 21 260 275 127 279 334 262 362 350 105 134 346 394 261 379 307 325 177 190
##
## Markers not placed on the map: 259 396 266 370 377 249 361 385 60 85 353
##
##
## Calculating LOD-Scores
## 259 --> AP3 : .......................
## 396 --> MgSTS483 : .......................
## 266 --> MgSTS24 : .......................
## 370 --> MgSTS583 : .......................
## 377 --> MgSTS631 : .......................
## 249 --> CC93 : .......................
## 361 --> MgSTS263 : .......................
## 385 --> MgSTS632 : .......................
## 60 --> BB216 : .......................
## 85 --> CA267 : .......................
## 353 --> MgSTS398 : .......................
##
##
## Placing remaining marker(s) at most likely position
## 385 --> MgSTS632 : .......................
## 377 --> MgSTS631 : ........................
## 370 --> MgSTS583 : .........................
## 396 --> MgSTS483 : ..........................
## 266 --> MgSTS24 : ...........................
## 85 --> CA267 : ............................
## 353 --> MgSTS398 : .............................
## 361 --> MgSTS263 : ..............................
## 259 --> AP3 : ...............................
## 249 --> CC93 : ................................
## 60 --> BB216 : .................................
##
## Estimating final genetic map using tol = 10E-5.LG1_2_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 100 CA150 0.00
## 236 CC320 11.03
## 308 MgSTS520 41.09
## 21 AA137 49.85
## 260 MgSTS17 54.47
## 275 MgSTS29 62.46
## 127 BD371 68.33
## 279 MgSTS133 74.15
## 334 MgSTS350 81.77
## 262 MgSTS18 93.86
## 362 MgSTS578 106.20
## 350 MgSTS500 109.99
## 105 CA75 112.49
## 134 BD251 123.43
## 346 MgSTS491 137.78
## 394 MgSTS494 156.35
## 261 MgSTS16 171.68
## 379 MgSTS562 179.22
## 307 MgSTS527 183.48
## 325 MgSTS341 188.70
## 177 AAT265 197.52
## 190 BC542 213.20
##
## 22 markers log-likelihood: -2825.297
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------
## | | 259 | 396 | 266 | 370 | 377 | 249 | 361 | 385 | 60 | 85 | 353 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | *** | | | | | | | | | | |
## | 100 | | | | | | | | | | | |
## | | * | | *** | | | | | | | | |
## | 236 | | | | | | | | | | | |
## | | | *** | | *** | | | | | | | |
## | 308 | | | | | | | | | | | |
## | | | | | | *** | | | | | | |
## | 21 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 260 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 275 | | | | | | | | | | | |
## | | | | | | | *** | *** | | | | |
## | 127 | | | | | | | | | | | |
## | | | | | | | ** | | | | | |
## | 279 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 334 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 262 | | | | | | | | | | | |
## | | | | | | | | | *** | | | |
## | 362 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 350 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 105 | | | | | | | | | | | |
## | | | | | | | | | | ** | | |
## | 134 | | | | | | | | | | | |
## | | | | | | | | | | *** | | |
## | 346 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 394 | | | | | | | | | | | |
## | | | | | | | | | | | *** | |
## | 261 | | | | | | | | | | | |
## | | | | | | | | | | | | *** |
## | 379 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 307 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 325 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 177 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## | 190 | | | | | | | | | | | |
## | | | | | | | | | | | | |
## -------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_1_2rm <- make_seq(LG1_2_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 259 AP3 0.00
## 100 CA150 3.21
## 236 CC320 12.17
## 370 MgSTS583 16.15
## 266 MgSTS24 21.21
## 396 MgSTS483 26.14
## 308 MgSTS520 56.46
## 377 MgSTS631 62.22
## 21 AA137 67.95
## 260 MgSTS17 71.71
## 275 MgSTS29 80.31
## 361 MgSTS263 82.81
## 127 BD371 90.50
## 249 CC93 90.50
## 279 MgSTS133 98.90
## 334 MgSTS350 106.57
## 262 MgSTS18 119.13
## 385 MgSTS632 124.52
## 362 MgSTS578 132.47
## 350 MgSTS500 136.46
## 105 CA75 138.78
## 134 BD251 152.54
## 60 BB216 154.14
## 346 MgSTS491 171.06
## 394 MgSTS494 189.95
## 85 CA267 197.83
## 261 MgSTS16 213.66
## 353 MgSTS398 217.02
## 379 MgSTS562 221.91
## 307 MgSTS527 226.15
## 325 MgSTS341 231.38
## 177 AAT265 240.21
## 190 BC542 256.00
##
## 33 markers log-likelihood: -3805.141HGL14<-rf_graph_table(Ligação_grupo_1_2rm, axis.cex=.6, inter=FALSE)
GL14<-Ligação_grupo_1_2rmThe same steps for subgroup 3 of the group 1
GL1_3<-make_seq(GL1_inicial, 3)
GL1_3##
## Number of markers: 26
## Markers in the sequence:
## BA449 BA387 BA196 BB124 BD340 BD100 BC374 BC526C CC61 CC53 MgSTS20 MgSTS19
## MgSTS26 MgSTS91 MgSTS93 CYCA aat356 MgSTS87 MgSTS360 MgSTS358 MgSTS344
## MgSTS471 MgSTS380 MgSTS561 MgSTS598 MgSTS620
##
## Parameters not estimated.LG1_3_f2 <- rcd(GL1_3)##
## order obtained using RCD algorithm:
##
## 263 277 338 404 270 278 250 219 26 31 265 406 355 320 251 128 69 43 147 380 339 287 286 288 337 199
##
## calculating multipoint map using tol = 1e-04 .LG1_3_f2##
## Printing map:
##
## Markers Position
##
## 263 MgSTS20 0.00
## 277 MgSTS91 3.29
## 338 MgSTS344 13.32
## 404 MgSTS598 15.51
## 270 MgSTS26 19.84
## 278 MgSTS93 21.00
## 250 CC61 27.37
## 219 BC526C 31.32
## 26 BA449 33.86
## 31 BA387 44.81
## 265 MgSTS19 54.71
## 406 MgSTS620 62.78
## 355 MgSTS380 77.92
## 320 MgSTS360 84.83
## 251 CC53 93.38
## 128 BD340 98.36
## 69 BB124 108.82
## 43 BA196 108.82
## 147 BD100 113.70
## 380 MgSTS561 119.08
## 339 MgSTS471 120.86
## 287 aat356 122.21
## 286 CYCA 122.21
## 288 MgSTS87 124.15
## 337 MgSTS358 144.02
## 199 BC374 175.25
##
## 26 markers log-likelihood: -2557.801LG1_3_f2_ord <- order_seq(input.seq = LG1_3_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 263 277 338 404 270 278 250 219 26 31 265 406 355 320 251 128 69 43 147 380 339 287 286 288 337 199
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
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##
##
##
## Running try algorithm
## 277 --> MgSTS91 : ......
## 270 --> MgSTS26 : .......
## 278 --> MgSTS93 : ........
## 406 --> MgSTS620 : ........
## 288 --> MgSTS87 : .........
## 265 --> MgSTS19 : .........
## 337 --> MgSTS358 : ..........
## 219 --> BC526C : ...........
## 338 --> MgSTS344 : ...........
## 404 --> MgSTS598 : ............
## 355 --> MgSTS380 : ............
## 287 --> aat356 : .............
## 286 --> CYCA : ..............
## 339 --> MgSTS471 : ..............
## 69 --> BB124 : ..............
## 26 --> BA449 : ...............
## 31 --> BA387 : ................
## 43 --> BA196 : .................
## 128 --> BD340 : .................
## 147 --> BD100 : ..................
## 251 --> CC53 : ...................
##
## LOD threshold = 3
##
## Positioned markers: 26 250 338 270 277 263 31 265 406 320 355 251 128 147 287 380 69 337 199
##
## Markers not placed on the map: 404 278 219 43 339 286 288
##
##
## Calculating LOD-Scores
## 404 --> MgSTS598 : ....................
## 278 --> MgSTS93 : ....................
## 219 --> BC526C : ....................
## 43 --> BA196 : ....................
## 339 --> MgSTS471 : ....................
## 286 --> CYCA : ....................
## 288 --> MgSTS87 : ....................
##
##
## Placing remaining marker(s) at most likely position
## 278 --> MgSTS93 : ....................
## 288 --> MgSTS87 : .....................
## 219 --> BC526C : ......................
## 339 --> MgSTS471 : .......................
## 404 --> MgSTS598 : ........................
## 43 --> BA196 : .........................
## 286 --> CYCA : ..........................
##
## Estimating final genetic map using tol = 10E-5.LG1_3_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 26 BA449 0.00
## 250 CC61 5.28
## 338 MgSTS344 14.82
## 270 MgSTS26 19.69
## 277 MgSTS91 26.24
## 263 MgSTS20 29.58
## 31 BA387 41.67
## 265 MgSTS19 50.90
## 406 MgSTS620 58.81
## 320 MgSTS360 70.01
## 355 MgSTS380 76.76
## 251 CC53 88.25
## 128 BD340 93.09
## 147 BD100 99.44
## 287 aat356 103.76
## 380 MgSTS561 105.59
## 69 BB124 112.35
## 337 MgSTS358 126.99
## 199 BC374 157.95
##
## 19 markers log-likelihood: -2237.837
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------
## | | 404 | 278 | 219 | 43 | 339 | 286 | 288 |
## |-----|-----|-----|-----|-----|-----|-----|-----|
## | | | | * | | | | |
## | 26 | | | | | | | |
## | | | | *** | | | | |
## | 250 | | | | | | | |
## | | *** | | | | | | |
## | 338 | | | | | | | |
## | | ** | *** | | | | | |
## | 270 | | | | | | | |
## | | | | | | | | |
## | 277 | | | | | | | |
## | | | | | | | | |
## | 263 | | | | | | | |
## | | | | | | | | |
## | 31 | | | | | | | |
## | | | | | | | | |
## | 265 | | | | | | | |
## | | | | | | | | |
## | 406 | | | | | | | |
## | | | | | | | | |
## | 320 | | | | | | | |
## | | | | | | | | |
## | 355 | | | | | | | |
## | | | | | | | | |
## | 251 | | | | | | | |
## | | | | | | | | |
## | 128 | | | | | | | |
## | | | | | | | | |
## | 147 | | | | | | | |
## | | | | | | * | ** | * |
## | 287 | | | | | | | |
## | | | | | | *** | *** | *** |
## | 380 | | | | | | | |
## | | | | | *** | | | |
## | 69 | | | | | | | |
## | | | | | ** | | | |
## | 337 | | | | | | | |
## | | | | | | | | |
## | 199 | | | | | | | |
## | | | | | | | | |
## -------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_1_3 <- make_seq(LG1_3_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 26 BA449 0.00
## 219 BC526C 2.41
## 250 CC61 7.26
## 404 MgSTS598 16.54
## 338 MgSTS344 18.54
## 278 MgSTS93 22.60
## 270 MgSTS26 23.83
## 277 MgSTS91 30.25
## 263 MgSTS20 33.61
## 31 BA387 45.71
## 265 MgSTS19 54.95
## 406 MgSTS620 62.87
## 320 MgSTS360 74.11
## 355 MgSTS380 80.89
## 251 CC53 92.47
## 128 BD340 97.36
## 147 BD100 103.88
## 339 MgSTS471 108.72
## 286 CYCA 110.27
## 287 aat356 110.27
## 288 MgSTS87 112.04
## 380 MgSTS561 114.60
## 43 BA196 121.37
## 69 BB124 121.37
## 337 MgSTS358 136.05
## 199 BC374 167.02
##
## 26 markers log-likelihood: -2514.099#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_1_3, axis.cex=.6, inter=FALSE)
Ligação_grupo_1_3##
## Printing map:
##
## Markers Position
##
## 26 BA449 0.00
## 219 BC526C 2.41
## 250 CC61 7.26
## 404 MgSTS598 16.54
## 338 MgSTS344 18.54
## 278 MgSTS93 22.60
## 270 MgSTS26 23.83
## 277 MgSTS91 30.25
## 263 MgSTS20 33.61
## 31 BA387 45.71
## 265 MgSTS19 54.95
## 406 MgSTS620 62.87
## 320 MgSTS360 74.11
## 355 MgSTS380 80.89
## 251 CC53 92.47
## 128 BD340 97.36
## 147 BD100 103.88
## 339 MgSTS471 108.72
## 286 CYCA 110.27
## 287 aat356 110.27
## 288 MgSTS87 112.04
## 380 MgSTS561 114.60
## 43 BA196 121.37
## 69 BB124 121.37
## 337 MgSTS358 136.05
## 199 BC374 167.02
##
## 26 markers log-likelihood: -2514.099LG1_3_seq_f2_rm <- drop_marker(Ligação_grupo_1_3, c(380, 287, 250,26, 338))
LG1_3_rcd_f2_rm <- rcd(LG1_3_seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 404 278 270 219 277 263 31 265 406 355 320 251 128 339 288 286 147 43 69 337 199
##
## calculating multipoint map using tol = 1e-04 .LG1_3_rcd_f2_rm##
## Printing map:
##
## Markers Position
##
## 404 MgSTS598 0.00
## 278 MgSTS93 4.59
## 270 MgSTS26 5.79
## 219 BC526C 14.59
## 277 MgSTS91 19.45
## 263 MgSTS20 22.76
## 31 BA387 34.85
## 265 MgSTS19 44.16
## 406 MgSTS620 52.25
## 355 MgSTS380 67.50
## 320 MgSTS360 74.41
## 251 CC53 83.15
## 128 BD340 88.23
## 339 MgSTS471 98.14
## 288 MgSTS87 101.32
## 286 CYCA 102.67
## 147 BD100 107.41
## 43 BA196 112.30
## 69 BB124 112.30
## 337 MgSTS358 126.95
## 199 BC374 157.92
##
## 21 markers log-likelihood: -2294.461LG1_3_f2_ord_rm <- order_seq(input.seq = LG1_3_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 404 278 270 219 277 263 31 265 406 355 320 251 128 339 288 286 147 43 69 337 199
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 277 --> MgSTS91 : ......
## 270 --> MgSTS26 : .......
## 278 --> MgSTS93 : ........
## 406 --> MgSTS620 : ........
## 288 --> MgSTS87 : .........
## 265 --> MgSTS19 : .........
## 337 --> MgSTS358 : ..........
## 219 --> BC526C : ...........
## 355 --> MgSTS380 : ...........
## 339 --> MgSTS471 : ............
## 69 --> BB124 : ............
## 31 --> BA387 : .............
## 43 --> BA196 : ..............
## 128 --> BD340 : ..............
## 147 --> BD100 : ...............
## 251 --> CC53 : ................
##
## LOD threshold = 3
##
## Positioned markers: 404 270 277 263 31 265 406 320 355 251 128 147 286 69 337 199
##
## Markers not placed on the map: 278 219 339 288 43
##
##
## Calculating LOD-Scores
## 278 --> MgSTS93 : .................
## 219 --> BC526C : .................
## 339 --> MgSTS471 : .................
## 288 --> MgSTS87 : .................
## 43 --> BA196 : .................
##
##
## Placing remaining marker(s) at most likely position
## 219 --> BC526C : .................
## 278 --> MgSTS93 : ..................
## 339 --> MgSTS471 : ...................
## 288 --> MgSTS87 : ....................
## 43 --> BA196 : .....................
##
## Estimating final genetic map using tol = 10E-5.LG1_3_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 404 MgSTS598 0.00
## 270 MgSTS26 4.37
## 277 MgSTS91 10.83
## 263 MgSTS20 14.15
## 31 BA387 26.30
## 265 MgSTS19 35.53
## 406 MgSTS620 43.44
## 320 MgSTS360 54.66
## 355 MgSTS380 61.44
## 251 CC53 73.28
## 128 BD340 78.23
## 147 BD100 84.75
## 286 CYCA 88.96
## 69 BB124 94.68
## 337 MgSTS358 109.31
## 199 BC374 140.25
##
## 16 markers log-likelihood: -1994.559
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------
## | | 278 | 219 | 339 | 288 | 43 |
## |-----|-----|-----|-----|-----|-----|
## | | | | | | |
## | 404 | | | | | |
## | | ** | | | | |
## | 270 | | | | | |
## | | *** | | | | |
## | 277 | | | | | |
## | | | | | | |
## | 263 | | | | | |
## | | | *** | | | |
## | 31 | | | | | |
## | | | | | | |
## | 265 | | | | | |
## | | | | | | |
## | 406 | | | | | |
## | | | | | | |
## | 320 | | | | | |
## | | | | | | |
## | 355 | | | | | |
## | | | | | | |
## | 251 | | | | | |
## | | | | | | |
## | 128 | | | | | |
## | | | | | | |
## | 147 | | | | | |
## | | | | ** | ** | |
## | 286 | | | | | |
## | | | | *** | *** | *** |
## | 69 | | | | | |
## | | | | | | ** |
## | 337 | | | | | |
## | | | | | | |
## | 199 | | | | | |
## | | | | | | |
## -------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_1_3rm <- make_seq(LG1_3_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 404 MgSTS598 0.00
## 270 MgSTS26 4.26
## 278 MgSTS93 5.47
## 277 MgSTS91 12.16
## 263 MgSTS20 15.43
## 219 BC526C 21.87
## 31 BA387 33.42
## 265 MgSTS19 43.20
## 406 MgSTS620 51.11
## 320 MgSTS360 62.39
## 355 MgSTS380 69.19
## 251 CC53 80.73
## 128 BD340 85.56
## 147 BD100 91.90
## 288 MgSTS87 98.11
## 286 CYCA 99.50
## 339 MgSTS471 101.05
## 43 BA196 107.92
## 69 BB124 107.92
## 337 MgSTS358 123.08
## 199 BC374 154.04
##
## 21 markers log-likelihood: -2260.937HGL11<-rf_graph_table(Ligação_grupo_1_3rm, axis.cex=.6, inter=FALSE)
GL11<-Ligação_grupo_1_3rmORDERING MARKERS THE NEXT LINKAGE GROUP
the next step is to order the markers within group 3, We can do the same steps with the previou group
set_map_fun(type = c("kosambi"))
LG3_inicial_f2 <- make_seq(LGs_f2, 3)
LG3_inicial_f2##
## Number of markers: 87
## Too many markers - not printing their names
##
## Parameters not estimated.LG3_inicial_rcd_f2 <- rcd(LG3_inicial_f2)##
## order obtained using RCD algorithm:
##
## 149 184 364 88 217 255 130 218 3 125 229 102 53 118 115 32 120 92 237 131 313 413 391 231 319 372 322 235 72 168 200 356 341 142 71 40 138 238 162 365 10 116 165 112 7 119 221 405 211 193 56 197 397 326 349 269 70 133 82 175 171 58 357 393 22 299 376 95 153 124 323 329 305 408 108 256 295 366 360 25 228 386 179 64 104 301 340
##
## calculating multipoint map using tol = 1e-04 .LG3_inicial_f2_ord <- order_seq(input.seq = LG3_inicial_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 184 364 88 217 255 130 218 3 125 229 102 53 118 115 32 120 92 237 131 313 413 391 231 319 372 322 235 72 168 200 356 341 142 71 40 138 238 162 365 10 116 165 112 7 119 221 405 211 193 56 197 397 326 349 269 70 133 82 175 171 58 357 393 22 299 376 95 153 124 323 329 305 408 108 256 295 366 360 25 228 386 179 64 104 301 340 149
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 175 --> AAT374 : ......
## 386 --> MgSTS609 : ......
## 165 --> BB103C : ......
## 162 --> CA258C : ......
## 153 --> AA153C : ......
## 397 --> MgSTS383 : ......
## 372 --> MgSTS535 : ......
## 319 --> MgSTS95 : ......
## 269 --> MgSTS27 : ......
## 171 --> AAT278 : ......
## 360 --> MgSTS293 : ......
## 408 --> MgSTS511 : ......
## 413 --> MgSTS214 : ......
## 313 --> MgSTS474 : .......
## 364 --> MgSTS574B : ........
## 221 --> BC128C : .........
## 305 --> MgSTS70 : .........
## 218 --> BC586C : .........
## 365 --> MgSTS574a : ..........
## 179 --> AAT372 : ..........
## 341 --> MgSTS34 : ..........
## 349 --> MgSTS509 : ..........
## 168 --> AAT261 : ..........
## 295 --> MgSTS308 : ..........
## 301 --> MgSTS48 : ..........
## 299 --> MgSTS43 : ..........
## 340 --> MgSTS37 : ..........
## 357 --> MgSTS351 : ..........
## 326 --> MgSTS388 : ..........
## 322 --> MgSTS50 : ..........
## 323 --> MgSTS75 : ...........
## 366 --> MgSTS579 : ...........
## 329 --> MgSTS332 : ...........
## 256 --> AAT283 : ...........
## 255 --> AAT312 : ...........
## 356 --> MgSTS251 : ...........
## 393 --> MgSTS435 : ...........
## 405 --> MgSTS441 : ...........
## 72 --> BB102 : ...........
## 56 --> BB281 : ...........
## 115 --> CB187 : ...........
## 120 --> CB156 : ............
## 116 --> CB173 : ............
## 112 --> CB246 : ............
## 119 --> CB162 : ............
## 108 --> CB309 : ............
## 102 --> CA131 : ............
## 3 --> AA404 : .............
## 53 --> BA75 : ..............
## 25 --> BA497 : ...............
## 130 --> BD292 : ...............
## 125 --> BD429 : ...............
## 131 --> BD286 : ................
## 142 --> BD170 : .................
## 124 --> BD433 : .................
## 200 --> BC334 : .................
## 211 --> BC131 : .................
## 237 --> CC286 : .................
## 235 --> CC330 : ..................
## 228 --> CC392 : ..................
## 71 --> BB119 : ..................
## 70 --> BB122 : ..................
## 58 --> BB259 : ..................
## 64 --> BB190 : ..................
## 118 --> CB166 : ..................
## 88 --> CA238 : ..................
## 92 --> CA220 : ..................
## 82 --> CA289 : ...................
## 95 --> CA198 : ...................
## 104 --> CA96 : ...................
## 10 --> AA280 : ...................
## 22 --> AA100 : ...................
## 32 --> BA384 : ...................
## 40 --> BA220 : ...................
## 138 --> BD209 : ....................
## 133 --> BD263 : ....................
## 217 --> BC70 : ....................
## 193 --> BC498 : ....................
## 197 --> BC379 : ....................
## 229 --> CC387 : ....................
## 231 --> CC378 : ....................
## 238 --> CC283 : ....................
##
## LOD threshold = 3
##
## Positioned markers: 376 322 391 92 413 313 131 184 237 364 53 102 125 3 218 115 7 40 149
##
## Markers not placed on the map: 88 217 255 130 229 118 32 120 231 319 372 235 72 168 200 356 341 142 71 138 238 162 365 10 116 165 112 119 221 405 211 193 56 197 397 326 349 269 70 133 82 175 171 58 357 393 22 299 95 153 124 323 329 305 408 108 256 295 366 360 25 228 386 179 64 104 301 340
##
##
## Calculating LOD-Scores
## 88 --> CA238 : ....................
## 217 --> BC70 : ....................
## 255 --> AAT312 : ....................
## 130 --> BD292 : ....................
## 229 --> CC387 : ....................
## 118 --> CB166 : ....................
## 32 --> BA384 : ....................
## 120 --> CB156 : ....................
## 231 --> CC378 : ....................
## 319 --> MgSTS95 : ....................
## 372 --> MgSTS535 : ....................
## 235 --> CC330 : ....................
## 72 --> BB102 : ....................
## 168 --> AAT261 : ....................
## 200 --> BC334 : ....................
## 356 --> MgSTS251 : ....................
## 341 --> MgSTS34 : ....................
## 142 --> BD170 : ....................
## 71 --> BB119 : ....................
## 138 --> BD209 : ....................
## 238 --> CC283 : ....................
## 162 --> CA258C : ....................
## 365 --> MgSTS574a : ....................
## 10 --> AA280 : ....................
## 116 --> CB173 : ....................
## 165 --> BB103C : ....................
## 112 --> CB246 : ....................
## 119 --> CB162 : ....................
## 221 --> BC128C : ....................
## 405 --> MgSTS441 : ....................
## 211 --> BC131 : ....................
## 193 --> BC498 : ....................
## 56 --> BB281 : ....................
## 197 --> BC379 : ....................
## 397 --> MgSTS383 : ....................
## 326 --> MgSTS388 : ....................
## 349 --> MgSTS509 : ....................
## 269 --> MgSTS27 : ....................
## 70 --> BB122 : ....................
## 133 --> BD263 : ....................
## 82 --> CA289 : ....................
## 175 --> AAT374 : ....................
## 171 --> AAT278 : ....................
## 58 --> BB259 : ....................
## 357 --> MgSTS351 : ....................
## 393 --> MgSTS435 : ....................
## 22 --> AA100 : ....................
## 299 --> MgSTS43 : ....................
## 95 --> CA198 : ....................
## 153 --> AA153C : ....................
## 124 --> BD433 : ....................
## 323 --> MgSTS75 : ....................
## 329 --> MgSTS332 : ....................
## 305 --> MgSTS70 : ....................
## 408 --> MgSTS511 : ....................
## 108 --> CB309 : ....................
## 256 --> AAT283 : ....................
## 295 --> MgSTS308 : ....................
## 366 --> MgSTS579 : ....................
## 360 --> MgSTS293 : ....................
## 25 --> BA497 : ....................
## 228 --> CC392 : ....................
## 386 --> MgSTS609 : ....................
## 179 --> AAT372 : ....................
## 64 --> BB190 : ....................
## 104 --> CA96 : ....................
## 301 --> MgSTS48 : ....................
## 340 --> MgSTS37 : ....................
##
##
## Placing remaining marker(s) at most likely position
## 162 --> CA258C : ....................
## 200 --> BC334 : .....................
## 319 --> MgSTS95 : ......................
## 221 --> BC128C : .......................
## 168 --> AAT261 : ........................
## 372 --> MgSTS535 : .........................
## 72 --> BB102 : ..........................
## 138 --> BD209 : ...........................
## 120 --> CB156 : ............................
## 10 --> AA280 : .............................
## 365 --> MgSTS574a : ..............................
## 238 --> CC283 : ...............................
## 130 --> BD292 : ................................
## 165 --> BB103C : .................................
## 32 --> BA384 : ..................................
## 119 --> CB162 : ...................................
## 356 --> MgSTS251 : ....................................
## 231 --> CC378 : .....................................
## 116 --> CB173 : ......................................
## 71 --> BB119 : .......................................
## 25 --> BA497 : ........................................
## 217 --> BC70 : .........................................
## 118 --> CB166 : ..........................................
## 329 --> MgSTS332 : ...........................................
## 256 --> AAT283 : ............................................
## 142 --> BD170 : .............................................
## 179 --> AAT372 : ..............................................
## 112 --> CB246 : ...............................................
## 305 --> MgSTS70 : ................................................
## 108 --> CB309 : .................................................
## 295 --> MgSTS308 : ..................................................
## 408 --> MgSTS511 : ...................................................
## 366 --> MgSTS579 : ....................................................
## 95 --> CA198 : .....................................................
## 124 --> BD433 : ......................................................
## 88 --> CA238 : .......................................................
## 153 --> AA153C : ........................................................
## 340 --> MgSTS37 : .........................................................
## 64 --> BB190 : ..........................................................
## 104 --> CA96 : ...........................................................
## 193 --> BC498 : ............................................................
## 22 --> AA100 : .............................................................
## 82 --> CA289 : ..............................................................
## 386 --> MgSTS609 : ...............................................................
## 58 --> BB259 : ................................................................
## 341 --> MgSTS34 : .................................................................
## 133 --> BD263 : ..................................................................
## 301 --> MgSTS48 : ...................................................................
## 299 --> MgSTS43 : ....................................................................
## 360 --> MgSTS293 : .....................................................................
## 326 --> MgSTS388 : ......................................................................
## 405 --> MgSTS441 : .......................................................................
## 229 --> CC387 : ........................................................................
## 397 --> MgSTS383 : .........................................................................
## 323 --> MgSTS75 : ..........................................................................
## 357 --> MgSTS351 : ...........................................................................
## 56 --> BB281 : ............................................................................
## 228 --> CC392 : .............................................................................
## 269 --> MgSTS27 : ..............................................................................
## 393 --> MgSTS435 : ...............................................................................
## 197 --> BC379 : ................................................................................
## 255 --> AAT312 : .................................................................................
## 70 --> BB122 : ..................................................................................
## 235 --> CC330 : ...................................................................................
## 211 --> BC131 : ....................................................................................
## 175 --> AAT374 : .....................................................................................
## 171 --> AAT278 : ......................................................................................
## 349 --> MgSTS509 : .......................................................................................
##
## Estimating final genetic map using tol = 10E-5.LG3_inicial_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 376 MgSTS539 0.00
## 322 MgSTS50 64.59
## 391 MgSTS425 78.62
## 92 CA220 92.94
## 413 MgSTS214 98.19
## 313 MgSTS474 102.95
## 131 BD286 107.96
## 184 AG19 123.34
## 237 CC286 139.60
## 364 MgSTS574B 161.43
## 53 BA75 176.05
## 102 CA131 183.35
## 125 BD429 188.44
## 3 AA404 191.74
## 218 BC586C 198.17
## 115 CB187 210.77
## 7 AA361 281.98
## 40 BA220 302.04
## 149 BD68 336.10
##
## 19 markers log-likelihood: -2548.394
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
## | | 88 | 217 | 255 | 130 | 229 | 118 | 32 | 120 | 231 | 319 | 372 | 235 | 72 | 168 | 200 | 356 | 341 | 142 | 71 | 138 | 238 | 162 | 365 | 10 | 116 | 165 | 112 | 119 | 221 | 405 | 211 | 193 | 56 | 197 | 397 | 326 | 349 | 269 | 70 | 133 | 82 | 175 | 171 | 58 | 357 | 393 | 22 | 299 | 95 | 153 | 124 | 323 | 329 | 305 | 408 | 108 | 256 | 295 | 366 | 360 | 25 | 228 | 386 | 179 | 64 | 104 | 301 | 340 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | | | | | | | | | | | | * | | | | | | | | | | | | | | | | | | *** | *** | ** | *** | ** | *** | *** | *** | *** | ** | *** | *** | ** | ** | *** | ** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | * | *** | *** | *** | *** | *** | *** | *** |
## | 376 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | * | | | ** | | | | | | | | | | | | | | | | | | ** | ** | *** | ** | *** | ** | ** | ** | ** | *** | ** | ** | *** | *** | ** | *** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | *** | ** | ** | ** | ** | ** | ** | ** |
## | 322 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | *** | *** | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 391 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 92 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 413 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 313 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 131 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 184 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 237 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | ** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 364 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | *** | | | | | | * | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 53 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | ** | | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 102 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | *** | | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 125 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | ** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 3 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | * | *** | *** | *** | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 218 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | *** | * | * | ** | ** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 115 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | ** | | | * | * | | | | | | *** | *** | *** | *** | *** | *** | *** | | | | | | | *** | * | *** | *** | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | ** | | | | | | | * | ** | | | |
## | 7 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | * | ** | ** | *** | *** | *** | *** | *** | *** | * | *** | ** | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 40 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | * | | | * | | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 149 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_3_inicial <- make_seq(LG3_inicial_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 256 AAT283 0.00
## 305 MgSTS70 26.56
## 323 MgSTS75 33.20
## 329 MgSTS332 36.95
## 408 MgSTS511 43.51
## 108 CB309 50.73
## 124 BD433 75.32
## 405 MgSTS441 100.11
## 299 MgSTS43 121.49
## 22 AA100 124.66
## 393 MgSTS435 128.02
## 357 MgSTS351 128.42
## 153 AA153C 136.66
## 95 CA198 144.95
## 58 BB259 148.06
## 211 BC131 149.33
## 376 MgSTS539 152.28
## 269 MgSTS27 158.82
## 349 MgSTS509 160.52
## 326 MgSTS388 160.82
## 397 MgSTS383 161.91
## 70 BB122 165.26
## 175 AAT374 168.11
## 56 BB281 174.64
## 193 BC498 174.64
## 82 CA289 179.50
## 133 BD263 183.79
## 171 AAT278 189.14
## 197 BC379 201.29
## 340 MgSTS37 220.91
## 301 MgSTS48 223.82
## 104 CA96 228.83
## 228 CC392 245.04
## 25 BA497 253.90
## 360 MgSTS293 260.68
## 366 MgSTS579 265.88
## 295 MgSTS308 268.57
## 386 MgSTS609 276.54
## 179 AAT372 284.97
## 64 BB190 304.07
## 231 CC378 707.02
## 322 MgSTS50 712.58
## 372 MgSTS535 716.60
## 319 MgSTS95 721.45
## 391 MgSTS425 732.59
## 92 CA220 746.86
## 413 MgSTS214 752.08
## 313 MgSTS474 756.83
## 131 BD286 761.83
## 184 AG19 777.21
## 237 CC286 793.12
## 88 CA238 810.74
## 364 MgSTS574B 817.93
## 120 CB156 824.02
## 53 BA75 837.94
## 102 CA131 845.42
## 125 BD429 850.70
## 229 CC387 854.02
## 3 AA404 854.02
## 130 BD292 862.28
## 218 BC586C 870.28
## 118 CB166 877.57
## 32 BA384 883.83
## 255 AAT312 884.74
## 115 CB187 897.45
## 217 BC70 907.09
## 221 BC128C 1310.04
## 235 CC330 1367.96
## 72 BB102 1385.99
## 168 AAT261 1402.76
## 200 BC334 1413.22
## 356 MgSTS251 1422.70
## 341 MgSTS34 1431.42
## 142 BD170 1440.38
## 119 CB162 1451.27
## 7 AA361 1459.40
## 116 CB173 1463.97
## 165 BB103C 1465.09
## 71 BB119 1470.42
## 112 CB246 1475.15
## 138 BD209 1481.55
## 238 CC283 1486.66
## 162 CA258C 1489.87
## 365 MgSTS574a 1493.88
## 10 AA280 1499.41
## 40 BA220 1507.44
## 149 BD68 1541.57
##
## 87 markers log-likelihood: -8874.393#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_3_inicial, axis.cex=.6, inter=FALSE)
Ligação_grupo_3_inicial##
## Printing map:
##
## Markers Position
##
## 256 AAT283 0.00
## 305 MgSTS70 26.56
## 323 MgSTS75 33.20
## 329 MgSTS332 36.95
## 408 MgSTS511 43.51
## 108 CB309 50.73
## 124 BD433 75.32
## 405 MgSTS441 100.11
## 299 MgSTS43 121.49
## 22 AA100 124.66
## 393 MgSTS435 128.02
## 357 MgSTS351 128.42
## 153 AA153C 136.66
## 95 CA198 144.95
## 58 BB259 148.06
## 211 BC131 149.33
## 376 MgSTS539 152.28
## 269 MgSTS27 158.82
## 349 MgSTS509 160.52
## 326 MgSTS388 160.82
## 397 MgSTS383 161.91
## 70 BB122 165.26
## 175 AAT374 168.11
## 56 BB281 174.64
## 193 BC498 174.64
## 82 CA289 179.50
## 133 BD263 183.79
## 171 AAT278 189.14
## 197 BC379 201.29
## 340 MgSTS37 220.91
## 301 MgSTS48 223.82
## 104 CA96 228.83
## 228 CC392 245.04
## 25 BA497 253.90
## 360 MgSTS293 260.68
## 366 MgSTS579 265.88
## 295 MgSTS308 268.57
## 386 MgSTS609 276.54
## 179 AAT372 284.97
## 64 BB190 304.07
## 231 CC378 707.02
## 322 MgSTS50 712.58
## 372 MgSTS535 716.60
## 319 MgSTS95 721.45
## 391 MgSTS425 732.59
## 92 CA220 746.86
## 413 MgSTS214 752.08
## 313 MgSTS474 756.83
## 131 BD286 761.83
## 184 AG19 777.21
## 237 CC286 793.12
## 88 CA238 810.74
## 364 MgSTS574B 817.93
## 120 CB156 824.02
## 53 BA75 837.94
## 102 CA131 845.42
## 125 BD429 850.70
## 229 CC387 854.02
## 3 AA404 854.02
## 130 BD292 862.28
## 218 BC586C 870.28
## 118 CB166 877.57
## 32 BA384 883.83
## 255 AAT312 884.74
## 115 CB187 897.45
## 217 BC70 907.09
## 221 BC128C 1310.04
## 235 CC330 1367.96
## 72 BB102 1385.99
## 168 AAT261 1402.76
## 200 BC334 1413.22
## 356 MgSTS251 1422.70
## 341 MgSTS34 1431.42
## 142 BD170 1440.38
## 119 CB162 1451.27
## 7 AA361 1459.40
## 116 CB173 1463.97
## 165 BB103C 1465.09
## 71 BB119 1470.42
## 112 CB246 1475.15
## 138 BD209 1481.55
## 238 CC283 1486.66
## 162 CA258C 1489.87
## 365 MgSTS574a 1493.88
## 10 AA280 1499.41
## 40 BA220 1507.44
## 149 BD68 1541.57
##
## 87 markers log-likelihood: -8874.393We are going to create subgroup 1 of the group 3
set_map_fun(type = c("kosambi"))
GL3_inicial <- group(LG3_inicial_f2, LOD=6, max.rf=0.24)## Selecting markers:
## group 1
## ..........................
## group 2
## ...........................................................GL3_inicial## This is an object of class 'group'
## It was generated from the object "LG3_inicial_f2"
##
## Criteria used to assign markers to groups:
## LOD = 6 , Maximum recombination fraction = 0.24
##
## No. markers: 87
## No. groups: 2
## No. linked markers: 85
## No. unlinked markers: 2
##
## Printing groups:
## Group 1 : 26 markers
## AA404 BA384 BA75 CA238 CA220 CA131 CB187 CB166 CB156 BD429 BD292 BD286 AG19 BC70 BC586C CC387 CC378 CC286 AAT312 MgSTS474 MgSTS95 MgSTS50 MgSTS574B MgSTS535 MgSTS425 MgSTS214
##
## Group 2 : 59 markers
## AA361 AA280 AA100 BA497 BA220 BB281 BB259 BB190 BB122 BB119 BB102 CA289 CA198 CA96 CB309 CB246 CB173 CB162 BD433 BD263 BD209 BD170 AA153C CA258C BB103C AAT261 AAT278 AAT374 AAT372 BC498 BC379 BC334 BC131 CC392 CC330 CC283 AAT283 MgSTS27 MgSTS308 MgSTS43 MgSTS48 MgSTS70 MgSTS75 MgSTS388 MgSTS332 MgSTS37 MgSTS34 MgSTS509 MgSTS251 MgSTS351 MgSTS293 MgSTS574a MgSTS579 MgSTS539 MgSTS609 MgSTS435 MgSTS383 MgSTS441 MgSTS511
##
## Unlinked markers: 2 markers
## BD68 BC128CGL3_1<-make_seq(GL3_inicial, 1)
LG3_1_f2 <- rcd(GL3_1)##
## order obtained using RCD algorithm:
##
## 217 255 53 32 115 118 102 229 125 3 218 130 364 120 88 237 313 413 92 131 391 319 372 322 231 184
##
## calculating multipoint map using tol = 1e-04 .LG3_1_f2##
## Printing map:
##
## Markers Position
##
## 217 BC70 0.00
## 255 AAT312 15.44
## 53 BA75 21.69
## 32 BA384 21.69
## 115 CB187 34.33
## 118 CB166 34.33
## 102 CA131 50.93
## 229 CC387 54.07
## 125 BD429 55.97
## 3 AA404 59.22
## 218 BC586C 65.15
## 130 BD292 74.32
## 364 MgSTS574B 99.12
## 120 CB156 103.70
## 88 CA238 106.94
## 237 CC286 125.18
## 313 MgSTS474 138.63
## 413 MgSTS214 143.44
## 92 CA220 149.08
## 131 BD286 154.12
## 391 MgSTS425 170.37
## 319 MgSTS95 181.32
## 372 MgSTS535 186.16
## 322 MgSTS50 190.16
## 231 CC378 195.65
## 184 AG19 231.23
##
## 26 markers log-likelihood: -2886.809LG3_1_f2_ord <- order_seq(input.seq = LG3_1_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 217 255 53 32 115 118 102 229 125 3 218 130 364 120 88 237 313 413 92 131 391 319 372 322 231 184
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 391 --> MgSTS425 : ......
## 372 --> MgSTS535 : ......
## 319 --> MgSTS95 : .......
## 413 --> MgSTS214 : .......
## 313 --> MgSTS474 : ........
## 364 --> MgSTS574B : .........
## 218 --> BC586C : ..........
## 322 --> MgSTS50 : ...........
## 255 --> AAT312 : ...........
## 115 --> CB187 : ...........
## 3 --> AA404 : ...........
## 53 --> BA75 : ............
## 125 --> BD429 : .............
## 130 --> BD292 : ..............
## 237 --> CC286 : ...............
## 118 --> CB166 : ................
## 88 --> CA238 : ................
## 92 --> CA220 : ................
## 32 --> BA384 : .................
## 229 --> CC387 : .................
## 231 --> CC378 : .................
##
## LOD threshold = 3
##
## Positioned markers: 217 218 130 3 125 102 53 120 364 237 131 184 313 413 92 372
##
## Markers not placed on the map: 255 32 115 118 229 88 391 319 322 231
##
##
## Calculating LOD-Scores
## 255 --> AAT312 : .................
## 32 --> BA384 : .................
## 115 --> CB187 : .................
## 118 --> CB166 : .................
## 229 --> CC387 : .................
## 88 --> CA238 : .................
## 391 --> MgSTS425 : .................
## 319 --> MgSTS95 : .................
## 322 --> MgSTS50 : .................
## 231 --> CC378 : .................
##
##
## Placing remaining marker(s) at most likely position
## 391 --> MgSTS425 : .................
## 319 --> MgSTS95 : ..................
## 118 --> CB166 : ...................
## 231 --> CC378 : ....................
## 32 --> BA384 : .....................
## 322 --> MgSTS50 : ......................
## 115 --> CB187 : .......................
## 229 --> CC387 : ........................
## 255 --> AAT312 : .........................
## 88 --> CA238 : ..........................
##
## Estimating final genetic map using tol = 10E-5.LG3_1_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 217 BC70 0.00
## 218 BC586C 10.61
## 130 BD292 20.10
## 3 AA404 28.74
## 125 BD429 31.84
## 102 CA131 36.74
## 53 BA75 43.69
## 120 CB156 56.45
## 364 MgSTS574B 62.06
## 237 CC286 82.54
## 131 BD286 96.43
## 184 AG19 112.85
## 313 MgSTS474 128.69
## 413 MgSTS214 133.47
## 92 CA220 140.04
## 372 MgSTS535 161.52
##
## 16 markers log-likelihood: -1903.861
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------
## | | 255 | 32 | 115 | 118 | 229 | 88 | 391 | 319 | 322 | 231 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | * | | *** | | * | | | | | |
## | 217 | | | | | | | | | | |
## | | * | | * | *** | | | | | | |
## | 218 | | | | | | | | | | |
## | | | | | | | | | | | |
## | 130 | | | | | | | | | | |
## | | | *** | | | * | | | | | |
## | 3 | | | | | | | | | | |
## | | | | | | *** | | | | | |
## | 125 | | | | | | | | | | |
## | | *** | | | | * | | | | | |
## | 102 | | | | | | | | | | |
## | | ** | | | | | | | | | |
## | 53 | | | | | | | | | | |
## | | | | | | | *** | | | | |
## | 120 | | | | | | | | | | |
## | | | | | | | * | | | | |
## | 364 | | | | | | | | | | |
## | | | | | | | ** | | | | |
## | 237 | | | | | | | | | | |
## | | | | | | | | | | | |
## | 131 | | | | | | | | | | |
## | | | | | | | | | | | |
## | 184 | | | | | | | | | | |
## | | | | | | | | | | | |
## | 313 | | | | | | | | | | |
## | | | | | | | | | | | |
## | 413 | | | | | | | | | | |
## | | | | | | | | | | | |
## | 92 | | | | | | | | | | |
## | | | | | | | | *** | *** | * | *** |
## | 372 | | | | | | | | | | |
## | | | | | | | | | | *** | |
## -------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_3_1 <- make_seq(LG3_1_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 217 BC70 0.00
## 32 BA384 15.62
## 255 AAT312 16.67
## 118 CB166 26.53
## 115 CB187 30.51
## 218 BC586C 40.20
## 130 BD292 48.47
## 3 AA404 56.64
## 229 CC387 56.64
## 125 BD429 59.96
## 102 CA131 65.25
## 53 BA75 72.74
## 120 CB156 86.67
## 364 MgSTS574B 92.73
## 88 CA238 100.11
## 237 CC286 115.71
## 131 BD286 129.08
## 184 AG19 144.89
## 313 MgSTS474 160.77
## 413 MgSTS214 165.55
## 92 CA220 170.81
## 391 MgSTS425 185.20
## 319 MgSTS95 196.69
## 322 MgSTS50 200.82
## 372 MgSTS535 204.66
## 231 CC378 210.32
##
## 26 markers log-likelihood: -2761.078#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_3_1, axis.cex=.6, inter=FALSE)
Ligação_grupo_3_1##
## Printing map:
##
## Markers Position
##
## 217 BC70 0.00
## 32 BA384 15.62
## 255 AAT312 16.67
## 118 CB166 26.53
## 115 CB187 30.51
## 218 BC586C 40.20
## 130 BD292 48.47
## 3 AA404 56.64
## 229 CC387 56.64
## 125 BD429 59.96
## 102 CA131 65.25
## 53 BA75 72.74
## 120 CB156 86.67
## 364 MgSTS574B 92.73
## 88 CA238 100.11
## 237 CC286 115.71
## 131 BD286 129.08
## 184 AG19 144.89
## 313 MgSTS474 160.77
## 413 MgSTS214 165.55
## 92 CA220 170.81
## 391 MgSTS425 185.20
## 319 MgSTS95 196.69
## 322 MgSTS50 200.82
## 372 MgSTS535 204.66
## 231 CC378 210.32
##
## 26 markers log-likelihood: -2761.078LG3_1_seq_f2_rm <- drop_marker(Ligação_grupo_3_1, c( 32, 118, 88,229))
LG3_1_rcd_f2_rm <- rcd(LG3_1_seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 217 255 53 102 125 3 218 130 115 120 364 237 313 413 92 131 391 319 372 322 231 184
##
## calculating multipoint map using tol = 1e-04 .LG3_1_rcd_f2_rm##
## Printing map:
##
## Markers Position
##
## 217 BC70 0.00
## 255 AAT312 15.04
## 53 BA75 23.34
## 102 CA131 28.70
## 125 BD429 32.52
## 3 AA404 35.00
## 218 BC586C 39.62
## 130 BD292 47.95
## 115 CB187 65.21
## 120 CB156 94.60
## 364 MgSTS574B 100.36
## 237 CC286 119.32
## 313 MgSTS474 132.69
## 413 MgSTS214 137.53
## 92 CA220 143.19
## 131 BD286 148.25
## 391 MgSTS425 164.50
## 319 MgSTS95 175.44
## 372 MgSTS535 180.29
## 322 MgSTS50 184.28
## 231 CC378 189.77
## 184 AG19 225.35
##
## 22 markers log-likelihood: -2582.211LG3_1_f2_ord_rm <- order_seq(input.seq = LG3_1_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 217 255 53 102 125 3 218 130 115 120 364 237 313 413 92 131 391 319 372 322 231 184
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
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##
##
##
## Running try algorithm
## 372 --> MgSTS535 : ......
## 319 --> MgSTS95 : .......
## 413 --> MgSTS214 : ........
## 313 --> MgSTS474 : .........
## 364 --> MgSTS574B : ..........
## 218 --> BC586C : ...........
## 322 --> MgSTS50 : ............
## 255 --> AAT312 : ............
## 115 --> CB187 : .............
## 120 --> CB156 : .............
## 102 --> CA131 : .............
## 53 --> BA75 : ..............
## 125 --> BD429 : ..............
## 130 --> BD292 : ...............
## 131 --> BD286 : ...............
## 92 --> CA220 : ................
## 231 --> CC378 : .................
##
## LOD threshold = 3
##
## Positioned markers: 217 218 3 125 102 255 364 237 184 131 313 413 92 391 319 372 231
##
## Markers not placed on the map: 53 130 115 120 322
##
##
## Calculating LOD-Scores
## 53 --> BA75 : ..................
## 130 --> BD292 : ..................
## 115 --> CB187 : ..................
## 120 --> CB156 : ..................
## 322 --> MgSTS50 : ..................
##
##
## Placing remaining marker(s) at most likely position
## 120 --> CB156 : ..................
## 130 --> BD292 : ...................
## 53 --> BA75 : ....................
## 322 --> MgSTS50 : .....................
## 115 --> CB187 : ......................
##
## Estimating final genetic map using tol = 10E-5.LG3_1_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 217 BC70 0.00
## 218 BC586C 10.62
## 3 AA404 15.94
## 125 BD429 18.65
## 102 CA131 22.83
## 255 AAT312 31.47
## 364 MgSTS574B 55.06
## 237 CC286 76.89
## 184 AG19 93.06
## 131 BD286 108.46
## 313 MgSTS474 113.44
## 413 MgSTS214 118.18
## 92 CA220 123.39
## 391 MgSTS425 137.63
## 319 MgSTS95 148.73
## 372 MgSTS535 153.85
## 231 CC378 159.25
##
## 17 markers log-likelihood: -2065.371
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------
## | | 53 | 130 | 115 | 120 | 322 |
## |-----|-----|-----|-----|-----|-----|
## | | | | *** | | |
## | 217 | | | | | |
## | | | | ** | | |
## | 218 | | | | | |
## | | | *** | | | |
## | 3 | | | | | |
## | | | | | | |
## | 125 | | | | | |
## | | | | | | |
## | 102 | | | | | |
## | | | | | | |
## | 255 | | | | | |
## | | *** | | | *** | |
## | 364 | | | | | |
## | | | | | | |
## | 237 | | | | | |
## | | | | | | |
## | 184 | | | | | |
## | | | | | | |
## | 131 | | | | | |
## | | | | | | |
## | 313 | | | | | |
## | | | | | | |
## | 413 | | | | | |
## | | | | | | |
## | 92 | | | | | |
## | | | | | | |
## | 391 | | | | | |
## | | | | | | |
## | 319 | | | | | |
## | | | | | | *** |
## | 372 | | | | | |
## | | | | | | |
## | 231 | | | | | |
## | | | | | | |
## -------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_3_1rm <- make_seq(LG3_1_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 115 CB187 0.00
## 217 BC70 9.50
## 218 BC586C 18.17
## 130 BD292 26.13
## 3 AA404 33.41
## 125 BD429 36.05
## 102 CA131 40.23
## 255 AAT312 47.75
## 53 BA75 56.91
## 120 CB156 69.30
## 364 MgSTS574B 74.88
## 237 CC286 96.77
## 184 AG19 113.25
## 131 BD286 128.65
## 313 MgSTS474 133.65
## 413 MgSTS214 138.39
## 92 CA220 143.61
## 391 MgSTS425 157.89
## 319 MgSTS95 169.39
## 322 MgSTS50 173.53
## 372 MgSTS535 177.36
## 231 CC378 183.03
##
## 22 markers log-likelihood: -2459.585HGL3<-rf_graph_table(Ligação_grupo_3_1rm, axis.cex=.6, inter=FALSE)
GL3<-Ligação_grupo_3_1rmWe are going to create subgroup 1 of the group 3
set_map_fun(type = c("kosambi"))
LG3_inicial_f2 <- make_seq(LGs_f2, 3)
LG3_inicial_f2##
## Number of markers: 87
## Too many markers - not printing their names
##
## Parameters not estimated.LG3_inicial_rcd_f2 <- rcd(LG3_inicial_f2)##
## order obtained using RCD algorithm:
##
## 149 184 364 88 217 255 130 218 3 125 229 102 53 118 115 32 120 92 237 131 313 413 391 231 319 372 322 235 72 168 200 356 341 142 71 40 138 238 162 365 10 116 165 112 7 119 221 405 211 193 56 197 397 326 349 269 70 133 82 175 171 58 357 393 22 299 376 95 153 124 323 329 305 408 108 256 295 366 360 25 228 386 179 64 104 301 340
##
## calculating multipoint map using tol = 1e-04 .LG3_inicial_f2_ord <- order_seq(input.seq = LG3_inicial_rcd_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 184 364 88 217 255 130 218 3 125 229 102 53 118 115 32 120 92 237 131 313 413 391 231 319 372 322 235 72 168 200 356 341 142 71 40 138 238 162 365 10 116 165 112 7 119 221 405 211 193 56 197 397 326 349 269 70 133 82 175 171 58 357 393 22 299 376 95 153 124 323 329 305 408 108 256 295 366 360 25 228 386 179 64 104 301 340 149
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
|
| | 0%
|
|= | 2%
|
|== | 3%
|
|=== | 5%
|
|==== | 7%
|
|===== | 8%
|
|====== | 10%
|
|======== | 12%
|
|========= | 13%
|
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|=========== | 17%
|
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|============= | 20%
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|
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|
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|
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|
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|
|=============================================================== | 97%
|
|================================================================ | 98%
|
|=================================================================| 100%
##
##
##
## Running try algorithm
## 175 --> AAT374 : ......
## 386 --> MgSTS609 : ......
## 165 --> BB103C : ......
## 162 --> CA258C : ......
## 153 --> AA153C : ......
## 397 --> MgSTS383 : ......
## 372 --> MgSTS535 : ......
## 319 --> MgSTS95 : ......
## 269 --> MgSTS27 : ......
## 171 --> AAT278 : ......
## 360 --> MgSTS293 : ......
## 408 --> MgSTS511 : ......
## 413 --> MgSTS214 : ......
## 313 --> MgSTS474 : .......
## 364 --> MgSTS574B : ........
## 221 --> BC128C : .........
## 305 --> MgSTS70 : .........
## 218 --> BC586C : .........
## 365 --> MgSTS574a : ..........
## 179 --> AAT372 : ..........
## 341 --> MgSTS34 : ..........
## 349 --> MgSTS509 : ..........
## 168 --> AAT261 : ..........
## 295 --> MgSTS308 : ..........
## 301 --> MgSTS48 : ..........
## 299 --> MgSTS43 : ..........
## 340 --> MgSTS37 : ..........
## 357 --> MgSTS351 : ..........
## 326 --> MgSTS388 : ..........
## 322 --> MgSTS50 : ..........
## 323 --> MgSTS75 : ...........
## 366 --> MgSTS579 : ...........
## 329 --> MgSTS332 : ...........
## 256 --> AAT283 : ...........
## 255 --> AAT312 : ...........
## 356 --> MgSTS251 : ...........
## 393 --> MgSTS435 : ...........
## 405 --> MgSTS441 : ...........
## 72 --> BB102 : ...........
## 56 --> BB281 : ...........
## 115 --> CB187 : ...........
## 120 --> CB156 : ............
## 116 --> CB173 : ............
## 112 --> CB246 : ............
## 119 --> CB162 : ............
## 108 --> CB309 : ............
## 102 --> CA131 : ............
## 3 --> AA404 : .............
## 53 --> BA75 : ..............
## 25 --> BA497 : ...............
## 130 --> BD292 : ...............
## 125 --> BD429 : ...............
## 131 --> BD286 : ................
## 142 --> BD170 : .................
## 124 --> BD433 : .................
## 200 --> BC334 : .................
## 211 --> BC131 : .................
## 237 --> CC286 : .................
## 235 --> CC330 : ..................
## 228 --> CC392 : ..................
## 71 --> BB119 : ..................
## 70 --> BB122 : ..................
## 58 --> BB259 : ..................
## 64 --> BB190 : ..................
## 118 --> CB166 : ..................
## 88 --> CA238 : ..................
## 92 --> CA220 : ..................
## 82 --> CA289 : ...................
## 95 --> CA198 : ...................
## 104 --> CA96 : ...................
## 10 --> AA280 : ...................
## 22 --> AA100 : ...................
## 32 --> BA384 : ...................
## 40 --> BA220 : ...................
## 138 --> BD209 : ....................
## 133 --> BD263 : ....................
## 217 --> BC70 : ....................
## 193 --> BC498 : ....................
## 197 --> BC379 : ....................
## 229 --> CC387 : ....................
## 231 --> CC378 : ....................
## 238 --> CC283 : ....................
##
## LOD threshold = 3
##
## Positioned markers: 376 322 391 92 413 313 131 184 237 364 53 102 125 3 218 115 7 40 149
##
## Markers not placed on the map: 88 217 255 130 229 118 32 120 231 319 372 235 72 168 200 356 341 142 71 138 238 162 365 10 116 165 112 119 221 405 211 193 56 197 397 326 349 269 70 133 82 175 171 58 357 393 22 299 95 153 124 323 329 305 408 108 256 295 366 360 25 228 386 179 64 104 301 340
##
##
## Calculating LOD-Scores
## 88 --> CA238 : ....................
## 217 --> BC70 : ....................
## 255 --> AAT312 : ....................
## 130 --> BD292 : ....................
## 229 --> CC387 : ....................
## 118 --> CB166 : ....................
## 32 --> BA384 : ....................
## 120 --> CB156 : ....................
## 231 --> CC378 : ....................
## 319 --> MgSTS95 : ....................
## 372 --> MgSTS535 : ....................
## 235 --> CC330 : ....................
## 72 --> BB102 : ....................
## 168 --> AAT261 : ....................
## 200 --> BC334 : ....................
## 356 --> MgSTS251 : ....................
## 341 --> MgSTS34 : ....................
## 142 --> BD170 : ....................
## 71 --> BB119 : ....................
## 138 --> BD209 : ....................
## 238 --> CC283 : ....................
## 162 --> CA258C : ....................
## 365 --> MgSTS574a : ....................
## 10 --> AA280 : ....................
## 116 --> CB173 : ....................
## 165 --> BB103C : ....................
## 112 --> CB246 : ....................
## 119 --> CB162 : ....................
## 221 --> BC128C : ....................
## 405 --> MgSTS441 : ....................
## 211 --> BC131 : ....................
## 193 --> BC498 : ....................
## 56 --> BB281 : ....................
## 197 --> BC379 : ....................
## 397 --> MgSTS383 : ....................
## 326 --> MgSTS388 : ....................
## 349 --> MgSTS509 : ....................
## 269 --> MgSTS27 : ....................
## 70 --> BB122 : ....................
## 133 --> BD263 : ....................
## 82 --> CA289 : ....................
## 175 --> AAT374 : ....................
## 171 --> AAT278 : ....................
## 58 --> BB259 : ....................
## 357 --> MgSTS351 : ....................
## 393 --> MgSTS435 : ....................
## 22 --> AA100 : ....................
## 299 --> MgSTS43 : ....................
## 95 --> CA198 : ....................
## 153 --> AA153C : ....................
## 124 --> BD433 : ....................
## 323 --> MgSTS75 : ....................
## 329 --> MgSTS332 : ....................
## 305 --> MgSTS70 : ....................
## 408 --> MgSTS511 : ....................
## 108 --> CB309 : ....................
## 256 --> AAT283 : ....................
## 295 --> MgSTS308 : ....................
## 366 --> MgSTS579 : ....................
## 360 --> MgSTS293 : ....................
## 25 --> BA497 : ....................
## 228 --> CC392 : ....................
## 386 --> MgSTS609 : ....................
## 179 --> AAT372 : ....................
## 64 --> BB190 : ....................
## 104 --> CA96 : ....................
## 301 --> MgSTS48 : ....................
## 340 --> MgSTS37 : ....................
##
##
## Placing remaining marker(s) at most likely position
## 162 --> CA258C : ....................
## 200 --> BC334 : .....................
## 319 --> MgSTS95 : ......................
## 221 --> BC128C : .......................
## 168 --> AAT261 : ........................
## 372 --> MgSTS535 : .........................
## 72 --> BB102 : ..........................
## 138 --> BD209 : ...........................
## 120 --> CB156 : ............................
## 10 --> AA280 : .............................
## 365 --> MgSTS574a : ..............................
## 238 --> CC283 : ...............................
## 130 --> BD292 : ................................
## 165 --> BB103C : .................................
## 32 --> BA384 : ..................................
## 119 --> CB162 : ...................................
## 356 --> MgSTS251 : ....................................
## 231 --> CC378 : .....................................
## 116 --> CB173 : ......................................
## 71 --> BB119 : .......................................
## 25 --> BA497 : ........................................
## 217 --> BC70 : .........................................
## 118 --> CB166 : ..........................................
## 329 --> MgSTS332 : ...........................................
## 256 --> AAT283 : ............................................
## 142 --> BD170 : .............................................
## 179 --> AAT372 : ..............................................
## 112 --> CB246 : ...............................................
## 305 --> MgSTS70 : ................................................
## 108 --> CB309 : .................................................
## 295 --> MgSTS308 : ..................................................
## 408 --> MgSTS511 : ...................................................
## 366 --> MgSTS579 : ....................................................
## 95 --> CA198 : .....................................................
## 124 --> BD433 : ......................................................
## 88 --> CA238 : .......................................................
## 153 --> AA153C : ........................................................
## 340 --> MgSTS37 : .........................................................
## 64 --> BB190 : ..........................................................
## 104 --> CA96 : ...........................................................
## 193 --> BC498 : ............................................................
## 22 --> AA100 : .............................................................
## 82 --> CA289 : ..............................................................
## 386 --> MgSTS609 : ...............................................................
## 58 --> BB259 : ................................................................
## 341 --> MgSTS34 : .................................................................
## 133 --> BD263 : ..................................................................
## 301 --> MgSTS48 : ...................................................................
## 299 --> MgSTS43 : ....................................................................
## 360 --> MgSTS293 : .....................................................................
## 326 --> MgSTS388 : ......................................................................
## 405 --> MgSTS441 : .......................................................................
## 229 --> CC387 : ........................................................................
## 397 --> MgSTS383 : .........................................................................
## 323 --> MgSTS75 : ..........................................................................
## 357 --> MgSTS351 : ...........................................................................
## 56 --> BB281 : ............................................................................
## 228 --> CC392 : .............................................................................
## 269 --> MgSTS27 : ..............................................................................
## 393 --> MgSTS435 : ...............................................................................
## 197 --> BC379 : ................................................................................
## 255 --> AAT312 : .................................................................................
## 70 --> BB122 : ..................................................................................
## 235 --> CC330 : ...................................................................................
## 211 --> BC131 : ....................................................................................
## 175 --> AAT374 : .....................................................................................
## 171 --> AAT278 : ......................................................................................
## 349 --> MgSTS509 : .......................................................................................
##
## Estimating final genetic map using tol = 10E-5.LG3_inicial_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 376 MgSTS539 0.00
## 322 MgSTS50 64.59
## 391 MgSTS425 78.62
## 92 CA220 92.94
## 413 MgSTS214 98.19
## 313 MgSTS474 102.95
## 131 BD286 107.96
## 184 AG19 123.34
## 237 CC286 139.60
## 364 MgSTS574B 161.43
## 53 BA75 176.05
## 102 CA131 183.35
## 125 BD429 188.44
## 3 AA404 191.74
## 218 BC586C 198.17
## 115 CB187 210.77
## 7 AA361 281.98
## 40 BA220 302.04
## 149 BD68 336.10
##
## 19 markers log-likelihood: -2548.394
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
## | | 88 | 217 | 255 | 130 | 229 | 118 | 32 | 120 | 231 | 319 | 372 | 235 | 72 | 168 | 200 | 356 | 341 | 142 | 71 | 138 | 238 | 162 | 365 | 10 | 116 | 165 | 112 | 119 | 221 | 405 | 211 | 193 | 56 | 197 | 397 | 326 | 349 | 269 | 70 | 133 | 82 | 175 | 171 | 58 | 357 | 393 | 22 | 299 | 95 | 153 | 124 | 323 | 329 | 305 | 408 | 108 | 256 | 295 | 366 | 360 | 25 | 228 | 386 | 179 | 64 | 104 | 301 | 340 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | | | | | | | | | | | | * | | | | | | | | | | | | | | | | | | *** | *** | ** | *** | ** | *** | *** | *** | *** | ** | *** | *** | ** | ** | *** | ** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | *** | * | *** | *** | *** | *** | *** | *** | *** |
## | 376 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | * | | | ** | | | | | | | | | | | | | | | | | | ** | ** | *** | ** | *** | ** | ** | ** | ** | *** | ** | ** | *** | *** | ** | *** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | ** | *** | ** | ** | ** | ** | ** | ** | ** |
## | 322 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | *** | *** | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 391 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 92 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 413 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 313 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 131 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 184 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 237 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | ** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 364 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | *** | | | | | | * | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 53 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | ** | | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 102 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | *** | | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 125 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | ** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 3 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | * | *** | *** | *** | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 218 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | *** | * | * | ** | ** | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 115 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | ** | | | * | * | | | | | | *** | *** | *** | *** | *** | *** | *** | | | | | | | *** | * | *** | *** | *** | | | | | | | | | | | | | | | | | | | | | | | | | | | | ** | | | | | | | * | ** | | | |
## | 7 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | * | ** | ** | *** | *** | *** | *** | *** | *** | * | *** | ** | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 40 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | * | | | * | | * | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | 149 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_3_inicial <- make_seq(LG3_inicial_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 256 AAT283 0.00
## 305 MgSTS70 26.56
## 323 MgSTS75 33.20
## 329 MgSTS332 36.95
## 408 MgSTS511 43.51
## 108 CB309 50.73
## 124 BD433 75.32
## 405 MgSTS441 100.11
## 299 MgSTS43 121.49
## 22 AA100 124.66
## 393 MgSTS435 128.02
## 357 MgSTS351 128.42
## 153 AA153C 136.66
## 95 CA198 144.95
## 58 BB259 148.06
## 211 BC131 149.33
## 376 MgSTS539 152.28
## 269 MgSTS27 158.82
## 349 MgSTS509 160.52
## 326 MgSTS388 160.82
## 397 MgSTS383 161.91
## 70 BB122 165.26
## 175 AAT374 168.11
## 56 BB281 174.64
## 193 BC498 174.64
## 82 CA289 179.50
## 133 BD263 183.79
## 171 AAT278 189.14
## 197 BC379 201.29
## 340 MgSTS37 220.91
## 301 MgSTS48 223.82
## 104 CA96 228.83
## 228 CC392 245.04
## 25 BA497 253.90
## 360 MgSTS293 260.68
## 366 MgSTS579 265.88
## 295 MgSTS308 268.57
## 386 MgSTS609 276.54
## 179 AAT372 284.97
## 64 BB190 304.07
## 231 CC378 707.02
## 322 MgSTS50 712.58
## 372 MgSTS535 716.60
## 319 MgSTS95 721.45
## 391 MgSTS425 732.59
## 92 CA220 746.86
## 413 MgSTS214 752.08
## 313 MgSTS474 756.83
## 131 BD286 761.83
## 184 AG19 777.21
## 237 CC286 793.12
## 88 CA238 810.74
## 364 MgSTS574B 817.93
## 120 CB156 824.02
## 53 BA75 837.94
## 102 CA131 845.42
## 125 BD429 850.70
## 229 CC387 854.02
## 3 AA404 854.02
## 130 BD292 862.28
## 218 BC586C 870.28
## 118 CB166 877.57
## 32 BA384 883.83
## 255 AAT312 884.74
## 115 CB187 897.45
## 217 BC70 907.09
## 221 BC128C 1310.04
## 235 CC330 1367.96
## 72 BB102 1385.99
## 168 AAT261 1402.76
## 200 BC334 1413.22
## 356 MgSTS251 1422.70
## 341 MgSTS34 1431.42
## 142 BD170 1440.38
## 119 CB162 1451.27
## 7 AA361 1459.40
## 116 CB173 1463.97
## 165 BB103C 1465.09
## 71 BB119 1470.42
## 112 CB246 1475.15
## 138 BD209 1481.55
## 238 CC283 1486.66
## 162 CA258C 1489.87
## 365 MgSTS574a 1493.88
## 10 AA280 1499.41
## 40 BA220 1507.44
## 149 BD68 1541.57
##
## 87 markers log-likelihood: -8874.393#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_3_inicial, axis.cex=.6, inter=FALSE)
Ligação_grupo_3_inicial##
## Printing map:
##
## Markers Position
##
## 256 AAT283 0.00
## 305 MgSTS70 26.56
## 323 MgSTS75 33.20
## 329 MgSTS332 36.95
## 408 MgSTS511 43.51
## 108 CB309 50.73
## 124 BD433 75.32
## 405 MgSTS441 100.11
## 299 MgSTS43 121.49
## 22 AA100 124.66
## 393 MgSTS435 128.02
## 357 MgSTS351 128.42
## 153 AA153C 136.66
## 95 CA198 144.95
## 58 BB259 148.06
## 211 BC131 149.33
## 376 MgSTS539 152.28
## 269 MgSTS27 158.82
## 349 MgSTS509 160.52
## 326 MgSTS388 160.82
## 397 MgSTS383 161.91
## 70 BB122 165.26
## 175 AAT374 168.11
## 56 BB281 174.64
## 193 BC498 174.64
## 82 CA289 179.50
## 133 BD263 183.79
## 171 AAT278 189.14
## 197 BC379 201.29
## 340 MgSTS37 220.91
## 301 MgSTS48 223.82
## 104 CA96 228.83
## 228 CC392 245.04
## 25 BA497 253.90
## 360 MgSTS293 260.68
## 366 MgSTS579 265.88
## 295 MgSTS308 268.57
## 386 MgSTS609 276.54
## 179 AAT372 284.97
## 64 BB190 304.07
## 231 CC378 707.02
## 322 MgSTS50 712.58
## 372 MgSTS535 716.60
## 319 MgSTS95 721.45
## 391 MgSTS425 732.59
## 92 CA220 746.86
## 413 MgSTS214 752.08
## 313 MgSTS474 756.83
## 131 BD286 761.83
## 184 AG19 777.21
## 237 CC286 793.12
## 88 CA238 810.74
## 364 MgSTS574B 817.93
## 120 CB156 824.02
## 53 BA75 837.94
## 102 CA131 845.42
## 125 BD429 850.70
## 229 CC387 854.02
## 3 AA404 854.02
## 130 BD292 862.28
## 218 BC586C 870.28
## 118 CB166 877.57
## 32 BA384 883.83
## 255 AAT312 884.74
## 115 CB187 897.45
## 217 BC70 907.09
## 221 BC128C 1310.04
## 235 CC330 1367.96
## 72 BB102 1385.99
## 168 AAT261 1402.76
## 200 BC334 1413.22
## 356 MgSTS251 1422.70
## 341 MgSTS34 1431.42
## 142 BD170 1440.38
## 119 CB162 1451.27
## 7 AA361 1459.40
## 116 CB173 1463.97
## 165 BB103C 1465.09
## 71 BB119 1470.42
## 112 CB246 1475.15
## 138 BD209 1481.55
## 238 CC283 1486.66
## 162 CA258C 1489.87
## 365 MgSTS574a 1493.88
## 10 AA280 1499.41
## 40 BA220 1507.44
## 149 BD68 1541.57
##
## 87 markers log-likelihood: -8874.393set_map_fun(type = c("kosambi"))
SGL3_inicial <- group(LG3_inicial_f2, LOD=6, max.rf=0.24)## Selecting markers:
## group 1
## ..........................
## group 2
## ...........................................................SGL3_inicial## This is an object of class 'group'
## It was generated from the object "LG3_inicial_f2"
##
## Criteria used to assign markers to groups:
## LOD = 6 , Maximum recombination fraction = 0.24
##
## No. markers: 87
## No. groups: 2
## No. linked markers: 85
## No. unlinked markers: 2
##
## Printing groups:
## Group 1 : 26 markers
## AA404 BA384 BA75 CA238 CA220 CA131 CB187 CB166 CB156 BD429 BD292 BD286 AG19 BC70 BC586C CC387 CC378 CC286 AAT312 MgSTS474 MgSTS95 MgSTS50 MgSTS574B MgSTS535 MgSTS425 MgSTS214
##
## Group 2 : 59 markers
## AA361 AA280 AA100 BA497 BA220 BB281 BB259 BB190 BB122 BB119 BB102 CA289 CA198 CA96 CB309 CB246 CB173 CB162 BD433 BD263 BD209 BD170 AA153C CA258C BB103C AAT261 AAT278 AAT374 AAT372 BC498 BC379 BC334 BC131 CC392 CC330 CC283 AAT283 MgSTS27 MgSTS308 MgSTS43 MgSTS48 MgSTS70 MgSTS75 MgSTS388 MgSTS332 MgSTS37 MgSTS34 MgSTS509 MgSTS251 MgSTS351 MgSTS293 MgSTS574a MgSTS579 MgSTS539 MgSTS609 MgSTS435 MgSTS383 MgSTS441 MgSTS511
##
## Unlinked markers: 2 markers
## BD68 BC128CSGL3_2_inicial<-make_seq(GL3_inicial, 2)We are going to create subgroup 2 of the group 3
set_map_fun(type = c("kosambi"))
GL3_2_in <- group(SGL3_2_inicial, LOD=6, max.rf=0.14)## Selecting markers:
## group 1
## .................
## group 2
## ................................
## group 3
## .....GL3_2_in## This is an object of class 'group'
## It was generated from the object "SGL3_2_inicial"
##
## Criteria used to assign markers to groups:
## LOD = 6 , Maximum recombination fraction = 0.14
##
## No. markers: 59
## No. groups: 3
## No. linked markers: 54
## No. unlinked markers: 5
##
## Printing groups:
## Group 1 : 17 markers
## AA361 AA280 BA220 BB119 CB246 CB173 CB162 BD209 BD170 CA258C BB103C AAT261 BC334 CC283 MgSTS34 MgSTS251 MgSTS574a
##
## Group 2 : 32 markers
## AA100 BA497 BB281 BB259 BB122 CA289 CA198 CA96 BD263 AA153C AAT278 AAT374 AAT372 BC498 BC379 BC131 CC392 MgSTS27 MgSTS308 MgSTS43 MgSTS48 MgSTS388 MgSTS37 MgSTS509 MgSTS351 MgSTS293 MgSTS579 MgSTS539 MgSTS609 MgSTS435 MgSTS383 MgSTS441
##
## Group 3 : 5 markers
## CB309 MgSTS70 MgSTS75 MgSTS332 MgSTS511
##
## Unlinked markers: 5 markers
## BB190 BB102 BD433 CC330 AAT283GL3_2_1<-make_seq(GL3_2_in, 1)
LG3_2_1_f2 <- rcd(GL3_2_1)##
## order obtained using RCD algorithm:
##
## 119 7 112 165 116 10 365 162 238 138 40 71 142 341 356 200 168
##
## calculating multipoint map using tol = 1e-04 .LG3_2_1_f2##
## Printing map:
##
## Markers Position
##
## 119 CB162 0.00
## 7 AA361 10.54
## 112 CB246 19.64
## 165 BB103C 24.97
## 116 CB173 28.90
## 10 AA280 34.58
## 365 MgSTS574a 37.67
## 162 CA258C 41.54
## 238 CC283 45.06
## 138 BD209 50.94
## 40 BA220 58.46
## 71 BB119 65.99
## 142 BD170 65.99
## 341 MgSTS34 75.55
## 356 MgSTS251 84.31
## 200 BC334 93.76
## 168 AAT261 104.52
##
## 17 markers log-likelihood: -1631.963LG3_2_1_f2_ord <- order_seq(input.seq = LG3_2_1_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 119 7 112 165 116 10 365 162 238 138 40 71 142 341 356 200 168
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
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##
##
##
## Running try algorithm
## 165 --> BB103C : ......
## 162 --> CA258C : .......
## 365 --> MgSTS574a : ........
## 341 --> MgSTS34 : .........
## 356 --> MgSTS251 : ..........
## 112 --> CB246 : ...........
## 7 --> AA361 : ...........
## 200 --> BC334 : ...........
## 71 --> BB119 : ............
## 10 --> AA280 : ............
## 40 --> BA220 : .............
## 138 --> BD209 : ..............
##
## LOD threshold = 3
##
## Positioned markers: 238 162 365 10 40 119 165 116 142 341 356 200 168
##
## Markers not placed on the map: 7 112 138 71
##
##
## Calculating LOD-Scores
## 7 --> AA361 : ..............
## 112 --> CB246 : ..............
## 138 --> BD209 : ..............
## 71 --> BB119 : ..............
##
##
## Placing remaining marker(s) at most likely position
## 7 --> AA361 : ..............
## 138 --> BD209 : ...............
## 112 --> CB246 : ................
## 71 --> BB119 : .................
##
## Estimating final genetic map using tol = 10E-5.LG3_2_1_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 238 CC283 0.00
## 162 CA258C 4.35
## 365 MgSTS574a 8.26
## 10 AA280 12.22
## 40 BA220 18.05
## 119 CB162 23.00
## 165 BB103C 30.62
## 116 CB173 31.69
## 142 BD170 38.52
## 341 MgSTS34 47.73
## 356 MgSTS251 56.61
## 200 BC334 66.32
## 168 AAT261 77.20
##
## 13 markers log-likelihood: -1350.066
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------
## | | 7 | 112 | 138 | 71 |
## |-----|-----|-----|-----|-----|
## | | | * | *** | |
## | 238 | | | | |
## | | | | | |
## | 162 | | | | |
## | | | | | |
## | 365 | | | | |
## | | | | | |
## | 10 | | | | |
## | | | | | |
## | 40 | | | | |
## | | | | | |
## | 119 | | | | |
## | | | * | | |
## | 165 | | | | |
## | | | | | |
## | 116 | | | | |
## | | *** | *** | | ** |
## | 142 | | | | |
## | | | | | *** |
## | 341 | | | | |
## | | | | | |
## | 356 | | | | |
## | | | | | |
## | 200 | | | | |
## | | | | | |
## | 168 | | | | |
## | | | | | |
## -------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_3_2_1 <- make_seq(LG3_2_1_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 138 BD209 0.00
## 238 CC283 7.23
## 162 CA258C 11.54
## 365 MgSTS574a 15.45
## 10 AA280 19.43
## 40 BA220 25.29
## 119 CB162 29.22
## 112 CB246 38.60
## 165 BB103C 43.10
## 116 CB173 43.99
## 7 AA361 47.94
## 142 BD170 54.95
## 71 BB119 54.95
## 341 MgSTS34 64.79
## 356 MgSTS251 73.53
## 200 BC334 82.95
## 168 AAT261 93.71
##
## 17 markers log-likelihood: -1605.282#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_3_2_1, axis.cex=.6, inter=FALSE)
Ligação_grupo_3_2_1##
## Printing map:
##
## Markers Position
##
## 138 BD209 0.00
## 238 CC283 7.23
## 162 CA258C 11.54
## 365 MgSTS574a 15.45
## 10 AA280 19.43
## 40 BA220 25.29
## 119 CB162 29.22
## 112 CB246 38.60
## 165 BB103C 43.10
## 116 CB173 43.99
## 7 AA361 47.94
## 142 BD170 54.95
## 71 BB119 54.95
## 341 MgSTS34 64.79
## 356 MgSTS251 73.53
## 200 BC334 82.95
## 168 AAT261 93.71
##
## 17 markers log-likelihood: -1605.282LG3_2_1_seq_f2_rm <- drop_marker(Ligação_grupo_3_2_1, c( 71,165, 341))
LG3_2_1_rcd_f2_rm <- rcd(LG3_2_1_seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 119 142 112 7 40 10 116 365 162 238 138 356 200 168
##
## calculating multipoint map using tol = 1e-04 .LG3_2_1_rcd_f2_rm##
## Printing map:
##
## Markers Position
##
## 119 CB162 0.00
## 142 BD170 14.13
## 112 CB246 24.84
## 7 AA361 34.10
## 40 BA220 37.44
## 10 AA280 43.41
## 116 CB173 44.81
## 365 MgSTS574a 47.46
## 162 CA258C 51.48
## 238 CC283 55.55
## 138 BD209 62.32
## 356 MgSTS251 88.60
## 200 BC334 98.64
## 168 AAT261 109.91
##
## 14 markers log-likelihood: -1377.08LG3_2_1_f2_ord_rm <- order_seq(input.seq = LG3_2_1_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 119 142 112 7 40 10 116 365 162 238 138 356 200 168
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
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##
##
##
## Running try algorithm
## 162 --> CA258C : ......
## 356 --> MgSTS251 : .......
## 112 --> CB246 : ........
## 116 --> CB173 : ........
## 142 --> BD170 : ........
## 200 --> BC334 : .........
## 10 --> AA280 : ..........
## 40 --> BA220 : ..........
## 238 --> CC283 : ...........
##
## LOD threshold = 3
##
## Positioned markers: 119 40 138 162 365 7 142 356 200 168
##
## Markers not placed on the map: 112 10 116 238
##
##
## Calculating LOD-Scores
## 112 --> CB246 : ...........
## 10 --> AA280 : ...........
## 116 --> CB173 : ...........
## 238 --> CC283 : ...........
##
##
## Placing remaining marker(s) at most likely position
## 116 --> CB173 : ...........
## 10 --> AA280 : ............
## 112 --> CB246 : .............
## 238 --> CC283 : ..............
##
## Estimating final genetic map using tol = 10E-5.LG3_2_1_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 119 CB162 0.00
## 40 BA220 5.57
## 138 BD209 12.83
## 162 CA258C 17.10
## 365 MgSTS574a 21.23
## 7 AA361 27.48
## 142 BD170 36.44
## 356 MgSTS251 54.23
## 200 BC334 63.16
## 168 AAT261 74.22
##
## 10 markers log-likelihood: -1129.19
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------
## | | 112 | 10 | 116 | 238 |
## |-----|-----|-----|-----|-----|
## | | | | | |
## | 119 | | | | |
## | | | | | |
## | 40 | | | | |
## | | | | | * |
## | 138 | | | | |
## | | | | | *** |
## | 162 | | | | |
## | | | | | ** |
## | 365 | | | | |
## | | *** | *** | *** | |
## | 7 | | | | |
## | | | | | |
## | 142 | | | | |
## | | | | | |
## | 356 | | | | |
## | | | | | |
## | 200 | | | | |
## | | | | | |
## | 168 | | | | |
## | | | | | |
## -------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_3_2_1rm <- make_seq(LG3_2_1_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 119 CB162 0.00
## 40 BA220 5.50
## 138 BD209 12.61
## 238 CC283 18.08
## 162 CA258C 21.37
## 112 CB246 26.09
## 365 MgSTS574a 29.70
## 10 AA280 32.61
## 116 CB173 32.61
## 7 AA361 38.47
## 142 BD170 47.61
## 356 MgSTS251 65.96
## 200 BC334 74.79
## 168 AAT261 85.86
##
## 14 markers log-likelihood: -1345.181HGL7<-rf_graph_table(Ligação_grupo_3_2_1rm, axis.cex=.6, inter=FALSE)
GL7<-Ligação_grupo_3_2_1rmset_map_fun(type = c("kosambi"))
GL3_2_in <- group(SGL3_2_inicial, LOD=6, max.rf=0.14)## Selecting markers:
## group 1
## .................
## group 2
## ................................
## group 3
## .....GL3_2_in## This is an object of class 'group'
## It was generated from the object "SGL3_2_inicial"
##
## Criteria used to assign markers to groups:
## LOD = 6 , Maximum recombination fraction = 0.14
##
## No. markers: 59
## No. groups: 3
## No. linked markers: 54
## No. unlinked markers: 5
##
## Printing groups:
## Group 1 : 17 markers
## AA361 AA280 BA220 BB119 CB246 CB173 CB162 BD209 BD170 CA258C BB103C AAT261 BC334 CC283 MgSTS34 MgSTS251 MgSTS574a
##
## Group 2 : 32 markers
## AA100 BA497 BB281 BB259 BB122 CA289 CA198 CA96 BD263 AA153C AAT278 AAT374 AAT372 BC498 BC379 BC131 CC392 MgSTS27 MgSTS308 MgSTS43 MgSTS48 MgSTS388 MgSTS37 MgSTS509 MgSTS351 MgSTS293 MgSTS579 MgSTS539 MgSTS609 MgSTS435 MgSTS383 MgSTS441
##
## Group 3 : 5 markers
## CB309 MgSTS70 MgSTS75 MgSTS332 MgSTS511
##
## Unlinked markers: 5 markers
## BB190 BB102 BD433 CC330 AAT283GL3_2_2_in<-make_seq(GL3_2_in, 2)
GL3_2_3_in<-make_seq(GL3_2_in, 3)
str(GL3_2_3_in)## List of 6
## $ seq.num : int [1:5] 108 305 323 329 408
## $ seq.phases: num -1
## $ seq.rf : num -1
## $ seq.like : NULL
## $ data.name : chr "fake_f2_onemap"
## $ twopt : chr "twopts_f2"
## - attr(*, "class")= chr "sequence"GL3_2_2 <- add_marker(GL3_2_2_in, c(108, 305, 323, 329, 408))
GL3_2_2##
## Number of markers: 37
## Markers in the sequence:
## AA100 BA497 BB281 BB259 BB122 CA289 CA198 CA96 BD263 AA153C AAT278 AAT374
## AAT372 BC498 BC379 BC131 CC392 MgSTS27 MgSTS308 MgSTS43 MgSTS48 MgSTS388
## MgSTS37 MgSTS509 MgSTS351 MgSTS293 MgSTS579 MgSTS539 MgSTS609 MgSTS435
## MgSTS383 MgSTS441 CB309 MgSTS70 MgSTS75 MgSTS332 MgSTS511
##
## Parameters not estimated.Finally, we have the new subgroup 2 of the group 3 adding the markers (108, 305, 323, 329, 408) to group 2. Now repeat the previous steps for the creation of the previous linking groups.
LG3_2_2_f2 <- rcd(GL3_2_2)##
## order obtained using RCD algorithm:
##
## 25 228 179 386 295 366 360 340 301 104 197 56 193 211 133 70 326 349 397 269 175 82 171 58 357 393 22 299 376 95 153 405 323 329 305 408 108
##
## calculating multipoint map using tol = 1e-04 .LG3_2_2_f2##
## Printing map:
##
## Markers Position
##
## 25 BA497 0.00
## 228 CC392 10.46
## 179 AAT372 25.43
## 386 MgSTS609 33.51
## 295 MgSTS308 41.50
## 366 MgSTS579 44.29
## 360 MgSTS293 49.59
## 340 MgSTS37 64.95
## 301 MgSTS48 67.82
## 104 CA96 72.31
## 197 BC379 89.99
## 56 BB281 91.18
## 193 BC498 102.97
## 211 BC131 104.45
## 133 BD263 108.10
## 70 BB122 110.51
## 326 MgSTS388 113.01
## 349 MgSTS509 113.29
## 397 MgSTS383 114.54
## 269 MgSTS27 117.13
## 175 AAT374 122.95
## 82 CA289 127.92
## 171 AAT278 133.69
## 58 BB259 148.40
## 357 MgSTS351 151.99
## 393 MgSTS435 152.50
## 22 AA100 156.18
## 299 MgSTS43 159.15
## 376 MgSTS539 168.45
## 95 CA198 174.32
## 153 AA153C 182.91
## 405 MgSTS441 202.43
## 323 MgSTS75 243.41
## 329 MgSTS332 247.87
## 305 MgSTS70 252.91
## 408 MgSTS511 262.26
## 108 CB309 269.80
##
## 37 markers log-likelihood: -3644.489LG3_2_2_f2_ord <- order_seq(input.seq = LG3_2_2_f2, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 25 228 179 386 295 366 360 340 301 104 197 56 193 211 133 70 326 349 397 269 175 82 171 58 357 393 22 299 376 95 153 405 323 329 305 408 108
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
|
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##
##
##
## Running try algorithm
## 175 --> AAT374 : ......
## 386 --> MgSTS609 : ......
## 153 --> AA153C : .......
## 269 --> MgSTS27 : .......
## 171 --> AAT278 : .......
## 360 --> MgSTS293 : ........
## 376 --> MgSTS539 : .........
## 408 --> MgSTS511 : ..........
## 305 --> MgSTS70 : ..........
## 179 --> AAT372 : ...........
## 349 --> MgSTS509 : ............
## 295 --> MgSTS308 : ............
## 301 --> MgSTS48 : .............
## 340 --> MgSTS37 : .............
## 357 --> MgSTS351 : .............
## 326 --> MgSTS388 : ..............
## 323 --> MgSTS75 : ..............
## 366 --> MgSTS579 : ...............
## 329 --> MgSTS332 : ................
## 393 --> MgSTS435 : ................
## 405 --> MgSTS441 : ................
## 56 --> BB281 : ................
## 211 --> BC131 : ................
## 228 --> CC392 : ................
## 70 --> BB122 : ................
## 58 --> BB259 : .................
## 82 --> CA289 : .................
## 95 --> CA198 : .................
## 22 --> AA100 : .................
## 133 --> BD263 : ..................
## 197 --> BC379 : ..................
## 193 --> BC498 : ...................
##
## LOD threshold = 3
##
## Positioned markers: 179 386 295 366 360 25 104 197 171 70 397 376 357 22 299 323 305 108
##
## Markers not placed on the map: 228 340 301 56 193 211 133 326 349 269 175 82 58 393 95 153 405 329 408
##
##
## Calculating LOD-Scores
## 228 --> CC392 : ...................
## 340 --> MgSTS37 : ...................
## 301 --> MgSTS48 : ...................
## 56 --> BB281 : ...................
## 193 --> BC498 : ...................
## 211 --> BC131 : ...................
## 133 --> BD263 : ...................
## 326 --> MgSTS388 : ...................
## 349 --> MgSTS509 : ...................
## 269 --> MgSTS27 : ...................
## 175 --> AAT374 : ...................
## 82 --> CA289 : ...................
## 58 --> BB259 : ...................
## 393 --> MgSTS435 : ...................
## 95 --> CA198 : ...................
## 153 --> AA153C : ...................
## 405 --> MgSTS441 : ...................
## 329 --> MgSTS332 : ...................
## 408 --> MgSTS511 : ...................
##
##
## Placing remaining marker(s) at most likely position
## 408 --> MgSTS511 : ...................
## 133 --> BD263 : ....................
## 58 --> BB259 : .....................
## 95 --> CA198 : ......................
## 405 --> MgSTS441 : .......................
## 329 --> MgSTS332 : ........................
## 56 --> BB281 : .........................
## 393 --> MgSTS435 : ..........................
## 82 --> CA289 : ...........................
## 301 --> MgSTS48 : ............................
## 228 --> CC392 : .............................
## 153 --> AA153C : ..............................
## 269 --> MgSTS27 : ...............................
## 349 --> MgSTS509 : ................................
## 175 --> AAT374 : .................................
## 193 --> BC498 : ..................................
## 326 --> MgSTS388 : ...................................
## 340 --> MgSTS37 : ....................................
## 211 --> BC131 : .....................................
##
## Estimating final genetic map using tol = 10E-5.LG3_2_2_f2_ord##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 179 AAT372 0.00
## 386 MgSTS609 8.52
## 295 MgSTS308 16.48
## 366 MgSTS579 19.18
## 360 MgSTS293 24.39
## 25 BA497 32.25
## 104 CA96 44.00
## 197 BC379 62.27
## 171 AAT278 75.27
## 70 BB122 80.62
## 397 MgSTS383 85.34
## 376 MgSTS539 91.79
## 357 MgSTS351 97.06
## 22 AA100 100.75
## 299 MgSTS43 103.98
## 323 MgSTS75 134.46
## 305 MgSTS70 142.09
## 108 CB309 156.41
##
## 18 markers log-likelihood: -2161.109
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------------------------------------------
## | | 228 | 340 | 301 | 56 | 193 | 211 | 133 | 326 | 349 | 269 | 175 | 82 | 58 | 393 | 95 | 153 | 405 | 329 | 408 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | ** | | | | | | | | | | | | | | | | | | |
## | 179 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | |
## | 386 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | |
## | 295 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | |
## | 366 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | |
## | 360 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | |
## | 25 | | | | | | | | | | | | | | | | | | | |
## | | *** | *** | *** | | | | | | | | | | | | | | | | |
## | 104 | | | | | | | | | | | | | | | | | | | |
## | | | ** | * | | | | | | | | | | | | | | | | |
## | 197 | | | | | | | | | | | | | | | | | | | |
## | | | | | *** | | | | | | | | | | | | | | | |
## | 171 | | | | | | | | | | | | | | | | | | | |
## | | | | | | ** | | *** | | | | ** | *** | | | | | | | |
## | 70 | | | | | | | | | | | | | | | | | | | |
## | | | | | | *** | | | *** | ** | ** | *** | * | | | | | | | |
## | 397 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | ** | | ** | *** | *** | | | | | | | | | |
## | 376 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | *** | | | | | | | *** | * | *** | | | | |
## | 357 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | *** | | *** | | | |
## | 22 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | |
## | 299 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | ** | *** | | |
## | 323 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | *** | |
## | 305 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | *** |
## | 108 | | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | | |
## -------------------------------------------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_3_2_2 <- make_seq(LG3_2_2_f2_ord, "force"))##
## Printing map:
##
## Markers Position
##
## 179 AAT372 0.00
## 386 MgSTS609 8.52
## 295 MgSTS308 16.47
## 366 MgSTS579 19.17
## 360 MgSTS293 24.37
## 25 BA497 31.02
## 228 CC392 39.71
## 340 MgSTS37 59.10
## 301 MgSTS48 61.91
## 104 CA96 66.40
## 197 BC379 84.53
## 56 BB281 84.54
## 171 AAT278 97.21
## 133 BD263 101.25
## 82 CA289 104.57
## 193 BC498 108.33
## 175 AAT374 112.33
## 70 BB122 115.15
## 397 MgSTS383 118.45
## 326 MgSTS388 119.54
## 349 MgSTS509 119.85
## 269 MgSTS27 121.55
## 376 MgSTS539 128.24
## 211 BC131 132.03
## 95 CA198 135.68
## 58 BB259 139.24
## 357 MgSTS351 141.93
## 393 MgSTS435 142.36
## 22 AA100 146.02
## 299 MgSTS43 149.09
## 153 AA153C 158.99
## 405 MgSTS441 178.36
## 323 MgSTS75 218.42
## 305 MgSTS70 225.48
## 329 MgSTS332 230.27
## 408 MgSTS511 236.69
## 108 CB309 243.87
##
## 37 markers log-likelihood: -3477.26#ripple_seq(Ligação_grupo_2, ws = 5, LOD = 6)
rf_graph_table(Ligação_grupo_3_2_2, axis.cex=.6, inter=FALSE)
Ligação_grupo_3_2_2##
## Printing map:
##
## Markers Position
##
## 179 AAT372 0.00
## 386 MgSTS609 8.52
## 295 MgSTS308 16.47
## 366 MgSTS579 19.17
## 360 MgSTS293 24.37
## 25 BA497 31.02
## 228 CC392 39.71
## 340 MgSTS37 59.10
## 301 MgSTS48 61.91
## 104 CA96 66.40
## 197 BC379 84.53
## 56 BB281 84.54
## 171 AAT278 97.21
## 133 BD263 101.25
## 82 CA289 104.57
## 193 BC498 108.33
## 175 AAT374 112.33
## 70 BB122 115.15
## 397 MgSTS383 118.45
## 326 MgSTS388 119.54
## 349 MgSTS509 119.85
## 269 MgSTS27 121.55
## 376 MgSTS539 128.24
## 211 BC131 132.03
## 95 CA198 135.68
## 58 BB259 139.24
## 357 MgSTS351 141.93
## 393 MgSTS435 142.36
## 22 AA100 146.02
## 299 MgSTS43 149.09
## 153 AA153C 158.99
## 405 MgSTS441 178.36
## 323 MgSTS75 218.42
## 305 MgSTS70 225.48
## 329 MgSTS332 230.27
## 408 MgSTS511 236.69
## 108 CB309 243.87
##
## 37 markers log-likelihood: -3477.26LG3_2_2_seq_f2_rm <- drop_marker(Ligação_grupo_3_2_2, c( 397, 171, 405))
LG3_2_2_rcd_f2_rm <- rcd(LG3_2_2_seq_f2_rm)##
## order obtained using RCD algorithm:
##
## 25 228 179 386 295 366 360 340 301 104 197 56 193 211 133 70 326 349 269 175 82 58 357 393 22 299 376 95 153 329 323 305 408 108
##
## calculating multipoint map using tol = 1e-04 .LG3_2_2_rcd_f2_rm##
## Printing map:
##
## Markers Position
##
## 25 BA497 0.00
## 228 CC392 10.46
## 179 AAT372 25.43
## 386 MgSTS609 33.51
## 295 MgSTS308 41.50
## 366 MgSTS579 44.29
## 360 MgSTS293 49.59
## 340 MgSTS37 64.95
## 301 MgSTS48 67.82
## 104 CA96 72.30
## 197 BC379 89.97
## 56 BB281 91.26
## 193 BC498 102.93
## 211 BC131 104.59
## 133 BD263 108.06
## 70 BB122 110.47
## 326 MgSTS388 112.75
## 349 MgSTS509 113.06
## 269 MgSTS27 114.86
## 175 AAT374 120.52
## 82 CA289 126.76
## 58 BB259 136.63
## 357 MgSTS351 139.24
## 393 MgSTS435 139.73
## 22 AA100 143.23
## 299 MgSTS43 146.02
## 376 MgSTS539 155.27
## 95 CA198 161.25
## 153 AA153C 169.86
## 329 MgSTS332 211.68
## 323 MgSTS75 215.28
## 305 MgSTS70 221.81
## 408 MgSTS511 231.25
## 108 CB309 238.82
##
## 34 markers log-likelihood: -3329.097LG3_2_2_f2_ord_rm <- order_seq(input.seq = LG3_2_2_rcd_f2_rm, n.init = 5,
subset.search = "twopt",
twopt.alg = "rcd", THRES = 3,
draw.try = FALSE, wait = 1)##
## Cross type: f2
## Choosing initial subset using 'two-point' approach
##
## order obtained using RCD algorithm:
##
## 25 228 179 386 295 366 360 340 301 104 197 56 193 211 133 70 326 349 269 175 82 58 357 393 22 299 376 95 153 329 323 305 408 108
##
## calculating multipoint map using tol = 0.1 .
##
##
## Comparing 60 orders:
##
##
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##
##
##
## Running try algorithm
## 175 --> AAT374 : ......
## 386 --> MgSTS609 : ......
## 153 --> AA153C : .......
## 269 --> MgSTS27 : .......
## 360 --> MgSTS293 : .......
## 376 --> MgSTS539 : .......
## 408 --> MgSTS511 : ........
## 305 --> MgSTS70 : ........
## 179 --> AAT372 : .........
## 295 --> MgSTS308 : ..........
## 340 --> MgSTS37 : ...........
## 357 --> MgSTS351 : ...........
## 326 --> MgSTS388 : ............
## 323 --> MgSTS75 : ............
## 366 --> MgSTS579 : .............
## 329 --> MgSTS332 : ..............
## 393 --> MgSTS435 : ..............
## 56 --> BB281 : ..............
## 211 --> BC131 : ...............
## 228 --> CC392 : ...............
## 70 --> BB122 : ...............
## 58 --> BB259 : ...............
## 104 --> CA96 : ...............
## 82 --> CA289 : ................
## 95 --> CA198 : ................
## 22 --> AA100 : ................
## 133 --> BD263 : .................
## 197 --> BC379 : .................
## 193 --> BC498 : .................
##
## LOD threshold = 3
##
## Positioned markers: 179 386 295 366 25 104 301 56 349 376 357 22 299 323 305 108
##
## Markers not placed on the map: 228 360 340 197 193 211 133 70 326 269 175 82 58 393 95 153 329 408
##
##
## Calculating LOD-Scores
## 228 --> CC392 : .................
## 360 --> MgSTS293 : .................
## 340 --> MgSTS37 : .................
## 197 --> BC379 : .................
## 193 --> BC498 : .................
## 211 --> BC131 : .................
## 133 --> BD263 : .................
## 70 --> BB122 : .................
## 326 --> MgSTS388 : .................
## 269 --> MgSTS27 : .................
## 175 --> AAT374 : .................
## 82 --> CA289 : .................
## 58 --> BB259 : .................
## 393 --> MgSTS435 : .................
## 95 --> CA198 : .................
## 153 --> AA153C : .................
## 329 --> MgSTS332 : .................
## 408 --> MgSTS511 : .................
##
##
## Placing remaining marker(s) at most likely position
## 175 --> AAT374 : .................
## 408 --> MgSTS511 : ..................
## 360 --> MgSTS293 : ...................
## 58 --> BB259 : ....................
## 95 --> CA198 : .....................
## 211 --> BC131 : ......................
## 269 --> MgSTS27 : .......................
## 329 --> MgSTS332 : ........................
## 326 --> MgSTS388 : .........................
## 393 --> MgSTS435 : ..........................
## 133 --> BD263 : ...........................
## 153 --> AA153C : ............................
## 228 --> CC392 : .............................
## 70 --> BB122 : ..............................
## 340 --> MgSTS37 : ...............................
## 82 --> CA289 : ................................
## 193 --> BC498 : .................................
## 197 --> BC379 : ..................................
##
## Estimating final genetic map using tol = 10E-5.LG3_2_2_f2_ord_rm##
## Best sequence found.
## Printing map:
##
## Markers Position
##
## 179 AAT372 0.00
## 386 MgSTS609 8.41
## 295 MgSTS308 16.11
## 366 MgSTS579 18.64
## 25 BA497 27.30
## 104 CA96 45.28
## 301 MgSTS48 48.94
## 56 BB281 63.34
## 349 MgSTS509 70.55
## 376 MgSTS539 76.00
## 357 MgSTS351 81.36
## 22 AA100 85.14
## 299 MgSTS43 88.35
## 323 MgSTS75 119.29
## 305 MgSTS70 126.93
## 108 CB309 141.25
##
## 16 markers log-likelihood: -1971.109
##
##
##
## The following markers could not be uniquely positioned.
## Printing most likely positions for each unpositioned marker:
##
## -------------------------------------------------------------------------------------------------------------------
## | | 228 | 360 | 340 | 197 | 193 | 211 | 133 | 70 | 326 | 269 | 175 | 82 | 58 | 393 | 95 | 153 | 329 | 408 |
## |-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
## | | | | | | | | | | | | | | | | | | | |
## | 179 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | |
## | 386 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | |
## | 295 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | |
## | 366 | | | | | | | | | | | | | | | | | | |
## | | ** | *** | | | | | | | | | | | | | | | | |
## | 25 | | | | | | | | | | | | | | | | | | |
## | | *** | | | | | | | | | | | | | | | | | |
## | 104 | | | | | | | | | | | | | | | | | | |
## | | | | ** | | | | | | | | | | | | | | | |
## | 301 | | | | | | | | | | | | | | | | | | |
## | | | | *** | *** | ** | | * | ** | | | | ** | | | | | | |
## | 56 | | | | | | | | | | | | | | | | | | |
## | | | | | ** | *** | | *** | *** | *** | *** | *** | *** | | | | | | |
## | 349 | | | | | | | | | | | | | | | | | | |
## | | | | | | | *** | | | | | | | | | | | | |
## | 376 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | *** | * | *** | | | |
## | 357 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | *** | | *** | | |
## | 22 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | |
## | 299 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | ** | | |
## | 323 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | *** | |
## | 305 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | *** |
## | 108 | | | | | | | | | | | | | | | | | | |
## | | | | | | | | | | | | | | | | | | | |
## -------------------------------------------------------------------------------------------------------------------
##
## '***' indicates the most likely position(s) (LOD = 0.0)
##
## '**' indicates very likely positions (LOD > -1.0)
##
## '*' indicates likely positions (LOD > -2.0)(Ligação_grupo_3_2_2rm <- make_seq(LG3_2_2_f2_ord_rm, "force"))##
## Printing map:
##
## Markers Position
##
## 179 AAT372 0.00
## 386 MgSTS609 8.52
## 295 MgSTS308 16.47
## 366 MgSTS579 19.16
## 360 MgSTS293 24.36
## 25 BA497 31.14
## 228 CC392 39.98
## 104 CA96 56.40
## 301 MgSTS48 61.42
## 340 MgSTS37 64.34
## 56 BB281 86.72
## 197 BC379 86.72
## 82 CA289 95.76
## 193 BC498 99.14
## 175 AAT374 103.02
## 133 BD263 106.38
## 70 BB122 107.98
## 326 MgSTS388 109.73
## 349 MgSTS509 110.03
## 269 MgSTS27 111.89
## 211 BC131 118.74
## 376 MgSTS539 122.02
## 95 CA198 127.56
## 58 BB259 130.60
## 357 MgSTS351 132.86
## 393 MgSTS435 133.30
## 22 AA100 136.87
## 299 MgSTS43 139.83
## 153 AA153C 149.76
## 323 MgSTS75 190.95
## 305 MgSTS70 198.02
## 329 MgSTS332 202.83
## 408 MgSTS511 209.25
## 108 CB309 216.42
##
## 34 markers log-likelihood: -3188.257HGL10<-rf_graph_table(Ligação_grupo_3_2_2rm, axis.cex=.6, inter=FALSE)
GL10<-Ligação_grupo_3_2_2rmAt lastly, we can to draw our GENETIC MAP
First we have to create a list of ordered linkage groups
maps <- list(GL1, GL2, GL3, GL4,GL5, GL6, GL7, GL8, GL9, GL10, GL11, GL12, GL13, GL14)Construct the linkage map
draw_map(maps, names= TRUE, grid=FALSE, cex.grp = 1, cex.mrk=.5)
heatmaps obtained of the linked groups
HGL1<-rf_graph_table(Ligação_grupo_1_1rm, axis.cex=.6, inter=FALSE)
HGL2<-rf_graph_table(Ligação_grupo_2, axis.cex=.6, inter=FALSE)
HGL3<-rf_graph_table(Ligação_grupo_3_1rm, axis.cex=.6, inter=FALSE)
HGL4<- rf_graph_table(Ligação_grupo_4rm, axis.cex=.6, inter=FALSE)
HGL5<-rf_graph_table(Ligação_grupo_5rm, axis.cex=.6, inter=FALSE)
HGL6<-rf_graph_table(Ligação_grupo_6rm, axis.cex=.6, inter=FALSE)
HGL7<-rf_graph_table(Ligação_grupo_3_2_1rm, axis.cex=.6, inter=FALSE)
HGL8<-rf_graph_table(Ligação_grupo_7, axis.cex=.6, inter=FALSE)
HGL9<-rf_graph_table(Ligação_grupo_8rm, axis.cex=.6, inter=FALSE)
HGL10<-rf_graph_table(Ligação_grupo_3_2_2rm, axis.cex=.6, inter=FALSE)
HGL11<-rf_graph_table(Ligação_grupo_1_3rm, axis.cex=.6, inter=FALSE)
HGL12<-rf_graph_table(Ligação_grupo_9rm, axis.cex=.6, inter=FALSE)
HGL13<-rf_graph_table(Ligação_grupo_10, axis.cex=.6, inter=FALSE)
HGL14<-rf_graph_table(Ligação_grupo_1_2rm, axis.cex=.6, inter=FALSE)