| blob | 4d5640ad1e570b148d3a9f5afc5aba31a2b95f1b |
3 ----------------------------------------------------
4 STRUCTURE by Pritchard, Stephens and Donnelly (2000)
5 and Falush, Stephens and Pritchard (2003)
6 Code by Pritchard, Falush and Hubisz
7 Version 2.3.2.1 (Oct 2009)
8 ----------------------------------------------------
12 Command line arguments: structure -e extraparams_admix_corre -K 3 -o output_admix_corre/output_admix_corre_K3_1
13 Input File: input.txt
15 Run parameters:
16 120 individuals
17 11 loci
18 3 populations assumed
19 10000000 Burn-in period
20 20000000 Reps
23 --------------------------------------------
24 Overall proportion of membership of the
25 sample in each of the 3 clusters
27 Inferred Clusters
28 1 2 3
29 0.435 0.127 0.438
31 --------------------------------------------
33 Allele-freq. divergence among pops (Net nucleotide distance),
34 computed using point estimates of P.
36 1 2 3
37 1 - 0.0721 0.0002
38 2 0.0721 - 0.0691
39 3 0.0002 0.0691 -
41 Average distances (expected heterozygosity) between individuals in same cluster:
42 cluster 1 : 0.7679
43 cluster 2 : 0.6798
44 cluster 3 : 0.7732
46 --------------------------------------------
47 Estimated Ln Prob of Data = -4320.0
48 Mean value of ln likelihood = -4192.2
49 Variance of ln likelihood = 255.6
50 Mean value of alpha = 0.0419
52 Mean value of Fst_1 = 0.0324
53 Mean value of Fst_2 = 0.2093
54 Mean value of Fst_3 = 0.0253
57 Inferred ancestry of individuals:
58 (%Miss) : Inferred clusters
59 1 (0) : 0.009 0.981 0.009
60 2 (0) : 0.010 0.979 0.011
61 3 (0) : 0.006 0.988 0.006
62 4 (0) : 0.005 0.990 0.005
63 5 (0) : 0.009 0.981 0.009
64 6 (9) : 0.017 0.967 0.016
65 7 (0) : 0.009 0.982 0.009
66 8 (0) : 0.042 0.920 0.038
67 9 (0) : 0.008 0.984 0.008
68 10 (0) : 0.010 0.980 0.010
69 11 (0) : 0.006 0.988 0.006
70 12 (0) : 0.015 0.969 0.016
71 13 (9) : 0.187 0.658 0.155
72 14 (0) : 0.006 0.987 0.006
73 15 (9) : 0.448 0.010 0.541
74 16 (27) : 0.434 0.015 0.551
75 17 (18) : 0.466 0.006 0.528
76 18 (9) : 0.501 0.017 0.482
77 19 (9) : 0.478 0.021 0.502
78 20 (0) : 0.448 0.014 0.537
79 21 (0) : 0.475 0.004 0.521
80 22 (9) : 0.444 0.041 0.515
81 23 (9) : 0.567 0.007 0.426
82 24 (9) : 0.436 0.014 0.550
83 25 (36) : 0.440 0.027 0.533
84 26 (27) : 0.497 0.042 0.461
85 27 (9) : 0.500 0.006 0.493
86 28 (27) : 0.442 0.009 0.549
87 29 (27) : 0.500 0.025 0.475
88 30 (0) : 0.458 0.009 0.533
89 31 (0) : 0.438 0.021 0.541
90 32 (0) : 0.561 0.003 0.436
91 33 (0) : 0.564 0.008 0.428
92 34 (0) : 0.517 0.008 0.475
93 35 (0) : 0.560 0.004 0.436
94 36 (18) : 0.548 0.009 0.443
95 37 (0) : 0.553 0.010 0.437
96 38 (0) : 0.555 0.009 0.436
97 39 (0) : 0.561 0.012 0.428
98 40 (0) : 0.548 0.006 0.446
99 41 (0) : 0.524 0.065 0.411
100 42 (36) : 0.469 0.028 0.503
101 43 (0) : 0.489 0.011 0.501
102 44 (0) : 0.528 0.009 0.462
103 45 (0) : 0.523 0.011 0.466
104 46 (0) : 0.475 0.031 0.495
105 47 (0) : 0.454 0.014 0.532
106 48 (0) : 0.560 0.008 0.432
107 49 (0) : 0.529 0.023 0.448
108 50 (0) : 0.502 0.009 0.489
109 51 (0) : 0.515 0.011 0.474
110 52 (0) : 0.456 0.008 0.536
111 53 (0) : 0.455 0.043 0.502
112 54 (9) : 0.568 0.008 0.424
113 55 (0) : 0.573 0.005 0.423
114 56 (0) : 0.572 0.004 0.424
115 57 (0) : 0.545 0.016 0.439
116 58 (0) : 0.566 0.007 0.427
117 59 (0) : 0.512 0.037 0.451
118 60 (0) : 0.457 0.015 0.528
119 61 (0) : 0.491 0.043 0.467
120 62 (0) : 0.533 0.009 0.457
121 63 (9) : 0.494 0.039 0.467
122 64 (0) : 0.564 0.009 0.426
123 65 (9) : 0.557 0.008 0.434
124 66 (0) : 0.533 0.008 0.458
125 67 (0) : 0.518 0.008 0.474
126 68 (0) : 0.572 0.005 0.424
127 69 (0) : 0.467 0.008 0.525
128 70 (9) : 0.570 0.005 0.425
129 71 (18) : 0.489 0.037 0.474
130 72 (9) : 0.550 0.020 0.430
131 73 (0) : 0.569 0.006 0.425
132 74 (0) : 0.550 0.006 0.444
133 75 (0) : 0.495 0.023 0.482
134 76 (18) : 0.568 0.006 0.426
135 77 (0) : 0.469 0.012 0.520
136 78 (0) : 0.540 0.008 0.452
137 79 (9) : 0.478 0.087 0.435
138 80 (0) : 0.486 0.004 0.510
139 81 (27) : 0.505 0.014 0.481
140 82 (27) : 0.514 0.012 0.474
141 83 (0) : 0.427 0.008 0.566
142 84 (0) : 0.419 0.078 0.503
143 85 (0) : 0.522 0.007 0.470
144 86 (36) : 0.507 0.022 0.472
145 87 (9) : 0.443 0.009 0.548
146 88 (0) : 0.426 0.028 0.546
147 89 (9) : 0.455 0.007 0.538
148 90 (18) : 0.442 0.021 0.536
149 91 (0) : 0.447 0.014 0.539
150 92 (0) : 0.452 0.038 0.510
151 93 (27) : 0.435 0.052 0.513
152 94 (27) : 0.493 0.008 0.498
153 95 (9) : 0.449 0.026 0.525
154 96 (18) : 0.424 0.019 0.557
155 97 (18) : 0.532 0.024 0.444
156 98 (18) : 0.470 0.011 0.518
157 99 (18) : 0.447 0.031 0.522
158 100 (27) : 0.437 0.019 0.544
159 101 (36) : 0.494 0.010 0.496
160 102 (18) : 0.421 0.014 0.566
161 103 (27) : 0.425 0.027 0.548
162 104 (9) : 0.449 0.011 0.540
163 105 (0) : 0.500 0.012 0.488
164 106 (9) : 0.500 0.007 0.493
165 107 (9) : 0.416 0.022 0.562
166 108 (9) : 0.438 0.009 0.553
167 109 (0) : 0.441 0.005 0.554
168 110 (9) : 0.424 0.006 0.570
169 111 (18) : 0.418 0.037 0.545
170 112 (18) : 0.434 0.021 0.545
171 113 (27) : 0.425 0.004 0.571
172 114 (27) : 0.450 0.018 0.532
173 115 (0) : 0.421 0.013 0.566
174 116 (36) : 0.443 0.019 0.538
175 117 (36) : 0.453 0.029 0.518
176 118 (0) : 0.421 0.015 0.564
177 119 (0) : 0.442 0.062 0.497
178 120 (18) : 0.453 0.047 0.500
181 Estimated Allele Frequencies in each cluster
182 First column gives estimated ancestral frequencies
185 Locus 1 :
186 17 alleles
187 1.7% missing data
188 172 (0.105) 0.113 0.079 0.113
189 184 (0.206) 0.180 0.445 0.188
190 200 (0.018) 0.009 0.066 0.011
191 188 (0.128) 0.273 0.112 0.232
192 180 (0.100) 0.090 0.078 0.093
193 176 (0.101) 0.073 0.175 0.080
194 192 (0.060) 0.041 0.008 0.046
195 220 (0.036) 0.030 0.005 0.032
196 168 (0.055) 0.050 0.007 0.053
197 216 (0.023) 0.035 0.003 0.032
198 196 (0.035) 0.021 0.005 0.025
199 208 (0.013) 0.007 0.002 0.008
200 212 (0.013) 0.008 0.002 0.008
201 244 (0.013) 0.011 0.002 0.011
202 164 (0.030) 0.016 0.004 0.020
203 160 (0.050) 0.035 0.008 0.039
204 224 (0.013) 0.007 0.002 0.008
206 Locus 2 :
207 4 alleles
208 6.7% missing data
209 180 (0.794) 0.797 0.748 0.797
210 182 (0.170) 0.167 0.247 0.168
211 178 (0.022) 0.028 0.003 0.025
212 184 (0.015) 0.009 0.002 0.010
214 Locus 3 :
215 12 alleles
216 6.7% missing data
217 201 (0.054) 0.045 0.249 0.047
218 213 (0.028) 0.014 0.100 0.017
219 211 (0.091) 0.097 0.375 0.095
220 215 (0.020) 0.010 0.067 0.012
221 209 (0.157) 0.155 0.116 0.156
222 203 (0.176) 0.164 0.024 0.168
223 205 (0.260) 0.307 0.038 0.296
224 193 (0.014) 0.008 0.002 0.009
225 199 (0.076) 0.075 0.011 0.076
226 207 (0.088) 0.099 0.013 0.097
227 191 (0.022) 0.019 0.003 0.019
228 195 (0.014) 0.007 0.002 0.009
230 Locus 4 :
231 15 alleles
232 5.8% missing data
233 187 (0.125) 0.120 0.480 0.122
234 183 (0.095) 0.098 0.204 0.098
235 173 (0.069) 0.070 0.074 0.069
236 179 (0.020) 0.014 0.148 0.015
237 191 (0.111) 0.127 0.015 0.122
238 195 (0.058) 0.040 0.008 0.045
239 205 (0.046) 0.054 0.006 0.052
240 193 (0.078) 0.119 0.012 0.108
241 181 (0.081) 0.076 0.012 0.078
242 185 (0.033) 0.034 0.004 0.034
243 177 (0.056) 0.055 0.007 0.056
244 189 (0.071) 0.069 0.010 0.070
245 175 (0.080) 0.071 0.011 0.073
246 197 (0.058) 0.040 0.008 0.046
247 207 (0.019) 0.011 0.002 0.013
249 Locus 5 :
250 9 alleles
251 9.2% missing data
252 211 (0.126) 0.081 0.433 0.093
253 199 (0.110) 0.124 0.044 0.120
254 203 (0.137) 0.115 0.177 0.122
255 207 (0.382) 0.438 0.284 0.423
256 215 (0.073) 0.073 0.040 0.074
257 219 (0.044) 0.040 0.006 0.040
258 223 (0.073) 0.099 0.010 0.090
259 195 (0.035) 0.019 0.004 0.023
260 227 (0.021) 0.011 0.003 0.014
262 Locus 6 :
263 7 alleles
264 15.0% missing data
265 307 (0.310) 0.375 0.525 0.359
266 303 (0.383) 0.393 0.343 0.392
267 311 (0.034) 0.042 0.064 0.038
268 299 (0.080) 0.048 0.043 0.057
269 295 (0.108) 0.086 0.015 0.091
270 291 (0.070) 0.048 0.009 0.054
271 287 (0.016) 0.008 0.002 0.010
273 Locus 7 :
274 6 alleles
275 24.2% missing data
276 187 (0.206) 0.222 0.276 0.218
277 195 (0.044) 0.026 0.193 0.030
278 191 (0.148) 0.143 0.115 0.145
279 179 (0.334) 0.351 0.256 0.346
280 183 (0.184) 0.174 0.149 0.176
281 175 (0.084) 0.084 0.011 0.085
283 Locus 8 :
284 8 alleles
285 9.2% missing data
286 219 (0.307) 0.347 0.291 0.336
287 223 (0.320) 0.251 0.571 0.270
288 215 (0.015) 0.007 0.061 0.009
289 227 (0.224) 0.260 0.060 0.252
290 231 (0.061) 0.079 0.008 0.073
291 239 (0.015) 0.008 0.002 0.009
292 235 (0.044) 0.041 0.006 0.041
293 243 (0.015) 0.008 0.002 0.009
295 Locus 9 :
296 13 alleles
297 2.5% missing data
298 171 (0.085) 0.060 0.219 0.067
299 173 (0.152) 0.135 0.093 0.140
300 175 (0.082) 0.057 0.502 0.062
301 183 (0.202) 0.185 0.097 0.190
302 181 (0.076) 0.164 0.034 0.139
303 179 (0.043) 0.024 0.006 0.030
304 187 (0.024) 0.015 0.003 0.017
305 177 (0.073) 0.052 0.010 0.058
306 165 (0.093) 0.144 0.013 0.132
307 169 (0.058) 0.053 0.009 0.055
308 167 (0.060) 0.082 0.008 0.077
309 189 (0.038) 0.021 0.005 0.025
310 163 (0.014) 0.007 0.002 0.008
312 Locus 10 :
313 8 alleles
314 2.5% missing data
315 256 (0.053) 0.045 0.105 0.046
316 250 (0.192) 0.255 0.295 0.238
317 252 (0.020) 0.010 0.340 0.012
318 254 (0.352) 0.348 0.208 0.352
319 258 (0.190) 0.179 0.026 0.183
320 248 (0.113) 0.085 0.015 0.092
321 246 (0.066) 0.070 0.009 0.068
322 244 (0.013) 0.007 0.002 0.008
324 Locus 11 :
325 16 alleles
326 7.5% missing data
327 214 (0.054) 0.053 0.330 0.053
328 218 (0.030) 0.020 0.228 0.022
329 204 (0.014) 0.007 0.030 0.008
330 224 (0.093) 0.069 0.141 0.074
331 226 (0.108) 0.091 0.064 0.096
332 210 (0.062) 0.064 0.092 0.062
333 222 (0.110) 0.098 0.044 0.102
334 220 (0.097) 0.109 0.013 0.106
335 216 (0.115) 0.127 0.015 0.126
336 228 (0.044) 0.093 0.006 0.080
337 212 (0.121) 0.137 0.017 0.134
338 230 (0.074) 0.086 0.011 0.084
339 206 (0.032) 0.020 0.005 0.023
340 208 (0.019) 0.011 0.003 0.013
341 234 (0.014) 0.007 0.002 0.008
342 232 (0.014) 0.007 0.002 0.009
344 Values of parameters used in structure:
345 DATAFILE=input.txt, OUTFILE=output_admix_corre/output_admix_corre_K3_1, NUMINDS=120, NUMLOCI=11, MISSING=0, LABEL=0, POPDATA=0, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=3, BURNIN=10000000, NUMREPS=20000000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=500, UPDATEFREQ=1000, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=1, PRINTLAMBDA=1, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.01000, PRINTQHAT=0, PRINTQSUM=1, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=0, PHASED=0, PLOIDY=2, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1434705072,
346 [STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,