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Pinf6_run_34_f
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----------------------------------------------------
STRUCTURE by Pritchard, Stephens and Donnelly (2000)
and Falush, Stephens and Pritchard (2003)
Code by Pritchard and Falush
Version 2.2 (March 2007)
----------------------------------------------------
Command line arguments: bin\structure.exe -m C:\Documents and Settings\grunwaldn\My Documents\Phytophthora clade 1c\SSR\structure\Pinf6\Pinf6\mainparams -e C:\Documents and Settings\grunwaldn\My Documents\Phytophthora clade 1c\SSR\structure\Pinf6\Pinf6\extraparams
Input File: C:\Documents and Settings\grunwaldn\My Documents\Phytophthora clade 1c\SSR\structure\Pinf6\project_data
Run parameters:
135 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: 0.005 0.013 0.974 0.009 17
2: 0.540 0.333 0.090 0.037 40
3: 0.064 0.069 0.008 0.859 48
4: 0.038 0.030 0.076 0.855 4
5: 0.921 0.035 0.010 0.034 21
6: 0.008 0.973 0.006 0.013 4
7: 0.027 0.926 0.011 0.036 1
--------------------------------------------
Allele-freq. divergence among pops (Net nucleotide distance),
computed using point estimates of P.
1 2 3 4
1 - 1.0267 1.2324 0.3355
2 1.0267 - 1.0555 0.5929
3 1.2324 1.0555 - 1.1118
4 0.3355 0.5929 1.1118 -
Average distances (expected heterozygosity) between individuals in same cluster:
cluster 1 : -2.6703
cluster 2 : -2.9286
cluster 3 : -2.8702
cluster 4 : -2.4959
--------------------------------------------
Estimated Ln Prob of Data = -3165.8
Mean value of ln likelihood = -3055.3
Variance of ln likelihood = 220.9
Mean value of alpha = 0.0360
Mean value of Fst_1 = 0.2216
Mean value of Fst_2 = 0.2738
Mean value of Fst_3 = 0.2589
Mean value of Fst_4 = 0.0768
Inferred ancestry of individuals:
Label (%Miss) Pop: Inferred clusters
1 PaEC1 (47) 1 : 0.003 0.005 0.988 0.004
2 PaEC10 (47) 1 : 0.003 0.003 0.990 0.004
3 PaEC11 (47) 1 : 0.003 0.004 0.983 0.011
4 PaEC12 (52) 1 : 0.003 0.004 0.990 0.003
5 PaEC13 (45) 1 : 0.010 0.006 0.953 0.031
6 PaEC14 (47) 1 : 0.004 0.005 0.987 0.004
7 PaEC15 (47) 1 : 0.004 0.007 0.986 0.004
8 PaEC2 (45) 1 : 0.003 0.004 0.990 0.003
9 PaEC3 (45) 1 : 0.003 0.003 0.990 0.003
10 PaEC4 (45) 1 : 0.004 0.004 0.988 0.004
11 PaEC5 (47) 1 : 0.004 0.113 0.879 0.004
12 PaEC6 (47) 1 : 0.004 0.009 0.983 0.004
13 PaEC7 (50) 1 : 0.003 0.003 0.991 0.003
14 PaEC8 (45) 1 : 0.019 0.019 0.907 0.055
15 PaEC9 (47) 1 : 0.003 0.004 0.990 0.003
16 PaPE1 (52) 1 : 0.004 0.012 0.980 0.004
17 PaPE2 (52) 1 : 0.004 0.013 0.979 0.004
18 PiCO1 (47) 2 : 0.982 0.005 0.004 0.010
19 PiCO2 (47) 2 : 0.983 0.005 0.003 0.009
20 PiCO3 (47) 2 : 0.981 0.005 0.003 0.010
21 PiCO4 (47) 2 : 0.982 0.005 0.003 0.010
22 PiCO5 (50) 2 : 0.040 0.006 0.184 0.770
23 PiEC1 (50) 2 : 0.974 0.006 0.004 0.016
24 PiEC10 (47) 2 : 0.005 0.978 0.012 0.005
25 PiEC11 (47) 2 : 0.006 0.983 0.006 0.006
26 PiEC12 (47) 2 : 0.007 0.981 0.005 0.007
27 PiEC13 (45) 2 : 0.006 0.984 0.004 0.006
28 PiEC14 (45) 2 : 0.006 0.985 0.004 0.005
29 PiEC2 (47) 2 : 0.890 0.041 0.004 0.064
30 PiEC3 (50) 2 : 0.979 0.005 0.004 0.012
31 PiEC4 (47) 2 : 0.004 0.007 0.984 0.004
32 PiEC5 (52) 2 : 0.004 0.011 0.972 0.013
33 PiEC6 (43) 2 : 0.034 0.785 0.019 0.162
34 PiEC7 (50) 2 : 0.018 0.230 0.705 0.047
35 PiEC8 (50) 2 : 0.007 0.403 0.483 0.107
36 PiPE1 (47) 2 : 0.989 0.003 0.003 0.004
37 PiPE10 (50) 2 : 0.963 0.020 0.009 0.007
38 PiPE11 (47) 2 : 0.985 0.004 0.005 0.006
39 PiPE12 (47) 2 : 0.986 0.004 0.005 0.005
40 PiPE13 (45) 2 : 0.977 0.012 0.005 0.006
41 PiPE14 (47) 2 : 0.985 0.005 0.005 0.005
42 PiPE2 (47) 2 : 0.970 0.010 0.005 0.015
43 PiPE20 (43) 2 : 0.057 0.913 0.009 0.021
44 PiPE21 (45) 2 : 0.012 0.973 0.005 0.010
45 PiPE22 (45) 2 : 0.004 0.987 0.004 0.005
46 PiPE23 (45) 2 : 0.012 0.952 0.015 0.021
47 PiPE24 (45) 2 : 0.004 0.986 0.004 0.005
48 PiPE25 (45) 2 : 0.004 0.986 0.004 0.005
49 PiPE26 (50) 2 : 0.963 0.021 0.009 0.007
50 PiPE27 (45) 2 : 0.007 0.979 0.005 0.009
51 PiPE3 (47) 2 : 0.966 0.005 0.004 0.024
52 PiPE4 (47) 2 : 0.976 0.008 0.005 0.012
53 PiPE5 (47) 2 : 0.983 0.005 0.004 0.009
54 PiPE6 (50) 2 : 0.933 0.006 0.049 0.012
55 PiPE7 (50) 2 : 0.962 0.007 0.023 0.008
56 PiPE8 (47) 2 : 0.969 0.010 0.006 0.015
57 PiPE9 (50) 2 : 0.983 0.004 0.004 0.009
58 PiMX1 (50) 3 : 0.065 0.035 0.005 0.896
59 PiMX10 (50) 3 : 0.010 0.022 0.017 0.950
60 PiMX11 (54) 3 : 0.072 0.010 0.004 0.914
61 PiMX12 (50) 3 : 0.034 0.011 0.038 0.917
62 PiMX13 (54) 3 : 0.047 0.010 0.004 0.939
63 PiMX14 (50) 3 : 0.015 0.017 0.006 0.961
64 PiMX15 (50) 3 : 0.006 0.949 0.023 0.022
65 PiMX16 (50) 3 : 0.357 0.038 0.007 0.597
66 PiMX17 (50) 3 : 0.008 0.027 0.006 0.959
67 PiMX18 (50) 3 : 0.046 0.322 0.008 0.624
68 PiMX19 (50) 3 : 0.011 0.108 0.003 0.878
69 PiMX2 (50) 3 : 0.012 0.026 0.004 0.958
70 PiMX20 (50) 3 : 0.015 0.103 0.012 0.870
71 PiMX21 (45) 3 : 0.014 0.019 0.003 0.964
72 PiMX22 (50) 3 : 0.008 0.010 0.019 0.963
73 PiMX23 (50) 3 : 0.238 0.007 0.005 0.751
74 PiMX24 (50) 3 : 0.038 0.005 0.005 0.952
75 PiMX25 (50) 3 : 0.072 0.049 0.005 0.874
76 PiMX26 (54) 3 : 0.019 0.024 0.009 0.948
77 PiMX27 (45) 3 : 0.013 0.008 0.011 0.968
78 PiMX28 (54) 3 : 0.042 0.080 0.016 0.863
79 PiMX29 (50) 3 : 0.378 0.118 0.007 0.498
80 PiMX3 (50) 3 : 0.007 0.005 0.006 0.982
81 PiMX30 (50) 3 : 0.007 0.010 0.004 0.978
82 PiMX4 (50) 3 : 0.013 0.006 0.006 0.975
83 PiMX40 (50) 3 : 0.005 0.010 0.005 0.980
84 PiMX41 (54) 3 : 0.012 0.942 0.004 0.042
85 PiMX42 (50) 3 : 0.909 0.005 0.003 0.083
86 PiMX43 (50) 3 : 0.007 0.010 0.004 0.979
87 PiMX44 (50) 3 : 0.007 0.011 0.004 0.978
88 PiMX45 (50) 3 : 0.008 0.009 0.004 0.979
89 PiMX46 (50) 3 : 0.008 0.010 0.004 0.979
90 PiMX47 (50) 3 : 0.008 0.009 0.004 0.979
91 PiMX48 (50) 3 : 0.108 0.010 0.007 0.874
92 PiMX49 (50) 3 : 0.107 0.010 0.008 0.876
93 PiMX5 (50) 3 : 0.010 0.008 0.003 0.979
94 PiMX50 (50) 3 : 0.111 0.010 0.008 0.872
95 PiMX6 (54) 3 : 0.021 0.006 0.004 0.968
96 PiMX7 (50) 3 : 0.013 0.005 0.003 0.979
97 PiMXT1 (50) 3 : 0.011 0.019 0.003 0.966
98 PiMXT2 (54) 3 : 0.009 0.016 0.006 0.969
99 PiMXT3 (50) 3 : 0.029 0.033 0.032 0.905
100 PiMXT4 (47) 3 : 0.006 0.006 0.003 0.985
101 PiMXT5 (50) 3 : 0.090 0.030 0.004 0.876
102 PiMXT6 (50) 3 : 0.007 0.019 0.008 0.966
103 PiMXT7 (54) 3 : 0.020 0.080 0.039 0.860
104 PiMXt48 (59) 3 : 0.013 0.007 0.004 0.975
105 PiMXt68 (50) 3 : 0.007 0.004 0.003 0.986
106 PiUS11 (47) 4 : 0.064 0.008 0.102 0.827
107 PiUS12 (50) 4 : 0.014 0.082 0.004 0.901
108 PiUS17 (54) 4 : 0.036 0.026 0.010 0.928
109 PiUS8 (50) 4 : 0.040 0.007 0.189 0.764
110 PiES1 (50) 5 : 0.989 0.003 0.003 0.005
111 PiES2 (50) 5 : 0.809 0.131 0.015 0.045
112 PiES3 (59) 5 : 0.945 0.024 0.024 0.007
113 PiHU1 (50) 5 : 0.982 0.007 0.007 0.005
114 PiHU2 (50) 5 : 0.925 0.019 0.010 0.047
115 PiNL1 (50) 5 : 0.868 0.006 0.006 0.120
116 PiNL2 (50) 5 : 0.910 0.017 0.007 0.066
117 PiPO1 (50) 5 : 0.985 0.004 0.006 0.005
118 PiPO2 (50) 5 : 0.970 0.006 0.004 0.020
119 PiSW1 (50) 5 : 0.985 0.004 0.004 0.007
120 PiSW2 (50) 5 : 0.920 0.008 0.003 0.069
121 PiUK1 (47) 5 : 0.780 0.059 0.007 0.155
122 PiUK10 (50) 5 : 0.980 0.007 0.007 0.006
123 PiUK2 (50) 5 : 0.965 0.021 0.006 0.009
124 PiUK3 (50) 5 : 0.938 0.032 0.016 0.014
125 PiUK4 (50) 5 : 0.934 0.035 0.016 0.015
126 PiUK5 (45) 5 : 0.955 0.020 0.006 0.018
127 PiUK6 (50) 5 : 0.937 0.038 0.009 0.016
128 PiUK7 (54) 5 : 0.707 0.255 0.017 0.021
129 PiUK8 (52) 5 : 0.914 0.011 0.025 0.050
130 PiUK9 (50) 5 : 0.952 0.018 0.008 0.021
131 PiVT1 (47) 6 : 0.005 0.981 0.005 0.010
132 PiVT2 (45) 6 : 0.010 0.964 0.007 0.020
133 PiVT3 (47) 6 : 0.007 0.983 0.004 0.006
134 PiVT4 (45) 6 : 0.011 0.964 0.008 0.017
135 PiSA1 (45) 7 : 0.027 0.926 0.011 0.036
Estimated Allele Frequencies in each cluster
First column gives estimated ancestral frequencies
Locus 1 :
10 alleles
98.9% missing data
160 (0.396) 0.157 0.921 0.776 0.413
158 (0.099) 0.004 0.015 0.188 0.089
162 (0.186) 0.750 0.022 0.014 0.299
154 (0.032) 0.001 0.022 0.002 0.004
164 (0.068) 0.025 0.004 0.005 0.053
170 (0.031) 0.001 0.003 0.002 0.012
152 (0.075) 0.056 0.005 0.006 0.054
166 (0.036) 0.001 0.002 0.002 0.023
156 (0.037) 0.002 0.002 0.003 0.023
150 (0.039) 0.002 0.002 0.003 0.032
Locus 2 :
26 alleles
104.1% missing data
108 (0.036) 0.002 0.003 0.573 0.009
152 (0.032) 0.010 0.002 0.049 0.004
148 (0.039) 0.002 0.003 0.024 0.036
150 (0.039) 0.002 0.002 0.047 0.015
138 (0.039) 0.002 0.179 0.028 0.012
142 (0.084) 0.058 0.191 0.152 0.037
146 (0.045) 0.019 0.003 0.080 0.015
136 (0.107) 0.466 0.167 0.007 0.193
132 (0.023) 0.023 0.001 0.002 0.003
112 (0.035) 0.002 0.002 0.003 0.118
134 (0.052) 0.084 0.047 0.003 0.023
144 (0.061) 0.008 0.251 0.005 0.080
118 (0.031) 0.134 0.004 0.002 0.011
154 (0.025) 0.144 0.002 0.002 0.003
140 (0.054) 0.002 0.119 0.004 0.116
158 (0.031) 0.010 0.002 0.002 0.016
184 (0.021) 0.001 0.002 0.001 0.013
174 (0.028) 0.001 0.002 0.002 0.024
176 (0.027) 0.001 0.002 0.002 0.024
110 (0.034) 0.003 0.003 0.003 0.074
164 (0.031) 0.002 0.003 0.002 0.064
188 (0.029) 0.001 0.002 0.002 0.045
190 (0.024) 0.001 0.001 0.002 0.024
104 (0.024) 0.001 0.002 0.002 0.024
172 (0.023) 0.001 0.001 0.001 0.013
130 (0.026) 0.021 0.003 0.002 0.004
Locus 3 :
3 alleles
100.0% missing data
203 (0.925) 0.910 0.995 0.995 0.982
209 (0.035) 0.001 0.002 0.002 0.013
206 (0.041) 0.088 0.002 0.003 0.005
Locus 4 :
4 alleles
100.7% missing data
166 (0.358) 0.357 0.432 0.231 0.362
170 (0.523) 0.414 0.559 0.761 0.592
160 (0.052) 0.102 0.003 0.003 0.014
168 (0.068) 0.127 0.005 0.005 0.032
Locus 5 :
21 alleles
86.7% missing data
209 (0.077) 0.003 0.006 0.183 0.127
247 (0.027) 0.001 0.002 0.166 0.003
287 (0.028) 0.001 0.002 0.016 0.003
251 (0.030) 0.001 0.002 0.076 0.003
263 (0.026) 0.001 0.002 0.076 0.003
267 (0.031) 0.001 0.002 0.076 0.004
213 (0.273) 0.293 0.580 0.153 0.533
235 (0.028) 0.001 0.002 0.015 0.004
261 (0.025) 0.001 0.002 0.015 0.003
265 (0.025) 0.001 0.002 0.015 0.003
255 (0.029) 0.001 0.002 0.061 0.003
283 (0.026) 0.001 0.002 0.046 0.003
269 (0.026) 0.001 0.002 0.014 0.004
273 (0.024) 0.001 0.002 0.014 0.004
281 (0.028) 0.001 0.002 0.014 0.004
271 (0.029) 0.001 0.002 0.046 0.003
205 (0.031) 0.263 0.002 0.001 0.004
217 (0.135) 0.412 0.294 0.006 0.225
225 (0.033) 0.001 0.002 0.002 0.049
221 (0.032) 0.002 0.071 0.002 0.008
215 (0.039) 0.011 0.020 0.002 0.005
Locus 6 :
7 alleles
101.9% missing data
176 (0.148) 0.144 0.432 0.496 0.030
186 (0.034) 0.001 0.002 0.024 0.004
178 (0.614) 0.846 0.536 0.465 0.734
174 (0.071) 0.003 0.021 0.006 0.078
172 (0.060) 0.002 0.004 0.004 0.115
182 (0.034) 0.001 0.002 0.002 0.014
168 (0.039) 0.002 0.002 0.003 0.024
Locus 7 :
25 alleles
95.2% missing data
128 (0.026) 0.001 0.001 0.196 0.007
202 (0.025) 0.001 0.001 0.115 0.003
130 (0.025) 0.001 0.001 0.251 0.003
160 (0.077) 0.112 0.021 0.146 0.069
166 (0.056) 0.072 0.005 0.024 0.047
200 (0.050) 0.002 0.251 0.164 0.012
156 (0.108) 0.396 0.095 0.023 0.336
152 (0.025) 0.001 0.265 0.002 0.003
162 (0.067) 0.048 0.140 0.005 0.052
164 (0.058) 0.003 0.025 0.039 0.071
150 (0.031) 0.011 0.013 0.003 0.007
204 (0.033) 0.004 0.014 0.003 0.022
140 (0.027) 0.097 0.001 0.002 0.004
148 (0.024) 0.055 0.001 0.002 0.003
154 (0.055) 0.091 0.036 0.004 0.032
198 (0.022) 0.001 0.017 0.002 0.003
170 (0.021) 0.001 0.018 0.001 0.003
158 (0.035) 0.010 0.002 0.003 0.033
206 (0.077) 0.054 0.061 0.005 0.179
208 (0.031) 0.033 0.004 0.002 0.011
212 (0.023) 0.001 0.017 0.002 0.003
210 (0.028) 0.001 0.001 0.002 0.048
266 (0.022) 0.001 0.001 0.002 0.012
246 (0.027) 0.001 0.004 0.003 0.019
132 (0.025) 0.001 0.002 0.002 0.020
Locus 8 :
3 alleles
99.6% missing data
174 (0.234) 0.306 0.017 0.441 0.205
176 (0.726) 0.692 0.981 0.556 0.772
154 (0.040) 0.002 0.003 0.003 0.023
Locus 9 :
3 alleles
93.3% missing data
148 (0.198) 0.097 0.311 0.379 0.064
151 (0.269) 0.124 0.348 0.584 0.124
157 (0.533) 0.779 0.342 0.038 0.811
Locus 10 :
3 alleles
101.5% missing data
192 (0.861) 0.886 0.501 0.990 0.927
189 (0.097) 0.005 0.496 0.007 0.067
195 (0.043) 0.110 0.003 0.003 0.005
Locus 11 :
13 alleles
101.9% missing data
181 (0.152) 0.472 0.128 0.811 0.035
183 (0.036) 0.001 0.002 0.104 0.004
179 (0.345) 0.427 0.833 0.049 0.546
197 (0.109) 0.040 0.009 0.009 0.208
199 (0.080) 0.041 0.006 0.006 0.069
191 (0.033) 0.002 0.002 0.003 0.013
203 (0.032) 0.001 0.002 0.002 0.013
201 (0.038) 0.002 0.003 0.003 0.023
213 (0.033) 0.001 0.003 0.003 0.013
205 (0.037) 0.001 0.002 0.003 0.023
209 (0.042) 0.002 0.003 0.003 0.033
207 (0.030) 0.001 0.002 0.002 0.013
195 (0.033) 0.009 0.003 0.003 0.006
Values of parameters used in structure:
DATAFILE=C:\Documents and Settings\grunwaldn\My Documents\Phytophthora clade 1c\SSR\structure\Pinf6\project_data, OUTFILE=C:\Documents and Settings\grunwaldn\My Documents\Phytophthora clade 1c\SSR\structure\Pinf6\Pinf6\Results\Pinf6_run_34, NUMINDS=135, 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, SEED=1241638497, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=4, PHASEINFO=0
[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,