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MX_two_run_40_f
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----------------------------------------------------
STRUCTURE by Pritchard, Stephens and Donnelly (2000)
and Falush, Stephens and Pritchard (2003)
Code by Pritchard, Falush and Hubisz
Version 2.3.4 (Jul 2012)
----------------------------------------------------
Command line arguments: bin/structure -m "/Users/maleja/Desktop/Structure/MX/MX/two/mainparams" -e "/Users/maleja/Desktop/Structure/MX/MX/two/extraparams"
Input File: /Users/maleja/Desktop/Structure/MX/MX/project_data
Run parameters:
48 individuals
11 loci
4 populations assumed
20000 Burn-in period
100000 Reps
--------------------------------------------
Proportion of membership of each pre-defined
population in each of the 4 clusters
Given Inferred Clusters Number of
Pop 1 2 3 4 Individuals
1: 0.167 0.281 0.204 0.347 48
--------------------------------------------
Allele-freq. divergence among pops (Net nucleotide distance),
computed using point estimates of P.
1 2 3 4
1 - 0.0748 0.0843 0.0697
2 0.0748 - 0.0582 0.0062
3 0.0843 0.0582 - 0.0367
4 0.0697 0.0062 0.0367 -
Average distances (expected heterozygosity) between individuals in same cluster:
cluster 1 : 0.3120
cluster 2 : 0.5201
cluster 3 : 0.4222
cluster 4 : 0.5667
--------------------------------------------
Estimated Ln Prob of Data = -1151.2
Mean value of ln likelihood = -1022.3
Variance of ln likelihood = 257.8
Mean value of alpha = 0.0642
Mean value of Fst_1 = 0.4880
Mean value of Fst_2 = 0.1058
Mean value of Fst_3 = 0.2181
Mean value of Fst_4 = 0.0234
Inferred ancestry of individuals:
Label (%Miss) Pop: Inferred clusters
1 PiMX1 (50) 1 : 0.039 0.581 0.131 0.248
2 PiMX10 (50) 1 : 0.015 0.121 0.558 0.307
3 PiMX11 (54) 1 : 0.148 0.240 0.322 0.290
4 PiMX12 (50) 1 : 0.013 0.292 0.083 0.612
5 PiMX13 (54) 1 : 0.382 0.059 0.445 0.113
6 PiMX14 (50) 1 : 0.163 0.267 0.173 0.398
7 PiMX15 (50) 1 : 0.034 0.330 0.057 0.580
8 PiMX16 (50) 1 : 0.019 0.109 0.571 0.301
9 PiMX17 (50) 1 : 0.079 0.672 0.032 0.218
10 PiMX18 (50) 1 : 0.049 0.422 0.187 0.343
11 PiMX19 (50) 1 : 0.014 0.477 0.042 0.467
12 PiMX2 (50) 1 : 0.056 0.233 0.036 0.675
13 PiMX20 (50) 1 : 0.032 0.287 0.032 0.649
14 PiMX21 (45) 1 : 0.021 0.241 0.050 0.687
15 PiMX22 (50) 1 : 0.024 0.266 0.054 0.656
16 PiMX23 (50) 1 : 0.029 0.247 0.123 0.600
17 PiMX24 (50) 1 : 0.150 0.156 0.449 0.245
18 PiMX25 (50) 1 : 0.399 0.177 0.142 0.283
19 PiMX26 (54) 1 : 0.045 0.501 0.056 0.397
20 PiMX27 (45) 1 : 0.128 0.155 0.274 0.444
21 PiMX28 (54) 1 : 0.182 0.082 0.560 0.177
22 PiMX29 (50) 1 : 0.021 0.186 0.027 0.766
23 PiMX3 (50) 1 : 0.012 0.149 0.236 0.603
24 PiMX30 (50) 1 : 0.028 0.086 0.648 0.238
25 PiMX4 (50) 1 : 0.009 0.185 0.126 0.680
26 PiMX40 (50) 1 : 0.179 0.272 0.156 0.393
27 PiMX41 (54) 1 : 0.190 0.283 0.077 0.451
28 PiMX42 (50) 1 : 0.090 0.161 0.416 0.332
29 PiMX43 (50) 1 : 0.972 0.009 0.010 0.009
30 PiMX44 (50) 1 : 0.969 0.010 0.012 0.009
31 PiMX45 (50) 1 : 0.970 0.010 0.012 0.009
32 PiMX46 (50) 1 : 0.970 0.010 0.011 0.009
33 PiMX47 (50) 1 : 0.971 0.010 0.011 0.008
34 PiMX48 (50) 1 : 0.013 0.011 0.965 0.011
35 PiMX49 (50) 1 : 0.013 0.011 0.965 0.011
36 PiMX5 (50) 1 : 0.062 0.707 0.014 0.217
37 PiMX50 (50) 1 : 0.013 0.012 0.966 0.010
38 PiMX6 (54) 1 : 0.057 0.395 0.027 0.521
39 PiMX7 (50) 1 : 0.061 0.703 0.017 0.220
40 PiMXT1 (50) 1 : 0.025 0.155 0.339 0.481
41 PiMXT2 (54) 1 : 0.023 0.254 0.265 0.457
42 PiMXT3 (50) 1 : 0.015 0.692 0.020 0.273
43 PiMXT4 (47) 1 : 0.025 0.514 0.015 0.446
44 PiMXT5 (50) 1 : 0.023 0.243 0.017 0.716
45 PiMXT6 (50) 1 : 0.028 0.712 0.031 0.229
46 PiMXT7 (54) 1 : 0.031 0.609 0.013 0.347
47 PiMXt48 (59) 1 : 0.098 0.623 0.020 0.259
48 PiMXt68 (50) 1 : 0.127 0.580 0.020 0.273
Estimated Allele Frequencies in each cluster
First column gives estimated ancestral frequencies
Locus 1 :
9 alleles
50.0% missing data
162 (0.310) 0.065 0.436 0.206 0.343
160 (0.377) 0.518 0.352 0.531 0.369
170 (0.028) 0.002 0.015 0.006 0.025
152 (0.043) 0.003 0.037 0.010 0.041
158 (0.057) 0.389 0.025 0.022 0.050
166 (0.044) 0.003 0.019 0.020 0.038
164 (0.053) 0.004 0.024 0.180 0.046
156 (0.044) 0.004 0.023 0.017 0.040
150 (0.044) 0.011 0.068 0.009 0.050
Locus 2 :
21 alleles
54.7% missing data
140 (0.083) 0.012 0.245 0.031 0.118
144 (0.089) 0.015 0.128 0.043 0.094
112 (0.094) 0.027 0.144 0.073 0.107
146 (0.028) 0.002 0.016 0.008 0.025
148 (0.047) 0.016 0.035 0.024 0.044
136 (0.108) 0.535 0.057 0.368 0.098
118 (0.034) 0.003 0.015 0.058 0.030
158 (0.026) 0.002 0.013 0.006 0.022
184 (0.028) 0.003 0.013 0.007 0.026
138 (0.031) 0.003 0.017 0.007 0.028
174 (0.042) 0.005 0.030 0.010 0.041
176 (0.038) 0.003 0.021 0.009 0.035
134 (0.043) 0.006 0.021 0.022 0.039
150 (0.029) 0.005 0.013 0.015 0.026
110 (0.049) 0.013 0.121 0.012 0.064
164 (0.039) 0.332 0.015 0.008 0.034
188 (0.060) 0.005 0.030 0.054 0.054
190 (0.040) 0.003 0.018 0.020 0.036
104 (0.032) 0.004 0.015 0.065 0.027
142 (0.030) 0.003 0.012 0.152 0.025
172 (0.028) 0.003 0.020 0.007 0.027
Locus 3 :
2 alleles
50.0% missing data
203 (0.963) 0.997 0.985 0.982 0.968
209 (0.037) 0.003 0.015 0.018 0.032
Locus 4 :
4 alleles
50.0% missing data
170 (0.512) 0.494 0.611 0.709 0.529
166 (0.333) 0.491 0.314 0.225 0.330
160 (0.063) 0.007 0.030 0.030 0.057
168 (0.092) 0.009 0.045 0.036 0.084
Locus 5 :
5 alleles
50.0% missing data
213 (0.468) 0.894 0.353 0.773 0.439
225 (0.058) 0.005 0.025 0.062 0.051
217 (0.280) 0.078 0.383 0.103 0.310
209 (0.162) 0.021 0.227 0.057 0.173
221 (0.031) 0.002 0.012 0.006 0.026
Locus 6 :
6 alleles
53.1% missing data
178 (0.688) 0.583 0.635 0.911 0.679
176 (0.064) 0.013 0.070 0.022 0.062
172 (0.107) 0.379 0.107 0.023 0.109
174 (0.064) 0.011 0.118 0.022 0.073
182 (0.037) 0.006 0.019 0.012 0.033
168 (0.041) 0.008 0.050 0.009 0.044
Locus 7 :
15 alleles
49.0% missing data
160 (0.091) 0.010 0.088 0.070 0.090
166 (0.042) 0.003 0.022 0.190 0.037
200 (0.027) 0.002 0.012 0.025 0.023
156 (0.244) 0.429 0.263 0.406 0.248
158 (0.045) 0.024 0.028 0.034 0.042
164 (0.102) 0.009 0.087 0.038 0.101
206 (0.124) 0.481 0.184 0.066 0.137
204 (0.039) 0.003 0.026 0.031 0.036
208 (0.039) 0.003 0.016 0.030 0.034
154 (0.050) 0.004 0.036 0.012 0.047
162 (0.066) 0.006 0.034 0.069 0.059
212 (0.025) 0.007 0.014 0.007 0.022
210 (0.046) 0.013 0.120 0.010 0.062
266 (0.026) 0.002 0.022 0.005 0.025
246 (0.033) 0.004 0.049 0.007 0.037
Locus 8 :
3 alleles
49.5% missing data
176 (0.743) 0.956 0.761 0.727 0.742
174 (0.212) 0.041 0.208 0.264 0.216
154 (0.045) 0.004 0.031 0.009 0.042
Locus 9 :
3 alleles
51.0% missing data
157 (0.736) 0.963 0.745 0.883 0.738
151 (0.186) 0.030 0.146 0.101 0.178
148 (0.078) 0.007 0.108 0.016 0.085
Locus 10 :
2 alleles
50.0% missing data
192 (0.825) 0.958 0.886 0.943 0.838
189 (0.175) 0.042 0.114 0.057 0.162
Locus 11 :
11 alleles
50.5% missing data
179 (0.400) 0.892 0.678 0.169 0.461
197 (0.196) 0.041 0.121 0.546 0.180
199 (0.091) 0.016 0.042 0.147 0.081
191 (0.034) 0.015 0.014 0.024 0.029
203 (0.032) 0.008 0.017 0.011 0.028
181 (0.042) 0.004 0.022 0.010 0.037
201 (0.046) 0.006 0.031 0.025 0.042
213 (0.029) 0.003 0.015 0.006 0.026
205 (0.044) 0.004 0.022 0.010 0.040
209 (0.056) 0.010 0.025 0.042 0.049
207 (0.031) 0.002 0.013 0.009 0.027
Values of parameters used in structure:
DATAFILE=/Users/maleja/Desktop/Structure/MX/MX/project_data, OUTFILE=/Users/maleja/Desktop/Structure/MX/MX/two/Results/two_run_40, NUMINDS=48, NUMLOCI=11, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=4, BURNIN=20000, NUMREPS=100000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTNET=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, 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=-1, PHASED=0, PLOIDY=4, PHASEINFO=0 LOCPRIOR=0, LOCPRIORINIT=1.000000, LOCDATA=0, LOCISPOP=0, LOCPRIORSTEP=0.100000, MAXLOCPRIOR=20.000000, SEED=1370296804,
[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,