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SA_New_run_19_f
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SA_New_run_19_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/SA/SA/New/mainparams" -e "/Users/maleja/Desktop/Structure/SA/SA/New/extraparams"
Input File: /Users/maleja/Desktop/Structure/SA/SA/project_data
Run parameters:
40 individuals
11 loci
2 populations assumed
20000 Burn-in period
100000 Reps
--------------------------------------------
Proportion of membership of each pre-defined
population in each of the 2 clusters
Given Inferred Clusters Number of
Pop 1 2 Individuals
1: 0.435 0.565 40
--------------------------------------------
Allele-freq. divergence among pops (Net nucleotide distance),
computed using point estimates of P.
1 2
1 - 0.1541
2 0.1541 -
Average distances (expected heterozygosity) between individuals in same cluster:
cluster 1 : 0.4936
cluster 2 : 0.4007
--------------------------------------------
Estimated Ln Prob of Data = -825.8
Mean value of ln likelihood = -799.2
Variance of ln likelihood = 53.4
Mean value of alpha = 0.0454
Mean value of Fst_1 = 0.0901
Mean value of Fst_2 = 0.2809
Inferred ancestry of individuals:
Label (%Miss) Pop: Inferred clusters
1 PiCO1 (47) 1 : 0.006 0.994
2 PiCO2 (47) 1 : 0.006 0.994
3 PiCO3 (47) 1 : 0.006 0.994
4 PiCO4 (47) 1 : 0.006 0.994
5 PiCO5 (50) 1 : 0.314 0.686
6 PiEC1 (50) 1 : 0.007 0.993
7 PiEC10 (47) 1 : 0.993 0.007
8 PiEC11 (47) 1 : 0.990 0.010
9 PiEC12 (47) 1 : 0.991 0.009
10 PiEC13 (45) 1 : 0.993 0.007
11 PiEC14 (45) 1 : 0.994 0.006
12 PiEC2 (47) 1 : 0.024 0.976
13 PiEC3 (50) 1 : 0.006 0.994
14 PiEC4 (47) 1 : 0.986 0.014
15 PiEC5 (52) 1 : 0.994 0.006
16 PiEC6 (43) 1 : 0.986 0.014
17 PiEC7 (50) 1 : 0.991 0.009
18 PiEC8 (50) 1 : 0.993 0.007
19 PiPE1 (47) 1 : 0.004 0.996
20 PiPE10 (50) 1 : 0.020 0.980
21 PiPE11 (47) 1 : 0.006 0.994
22 PiPE12 (47) 1 : 0.006 0.994
23 PiPE13 (45) 1 : 0.013 0.987
24 PiPE14 (47) 1 : 0.006 0.994
25 PiPE2 (47) 1 : 0.010 0.990
26 PiPE20 (43) 1 : 0.988 0.012
27 PiPE21 (45) 1 : 0.957 0.043
28 PiPE22 (45) 1 : 0.994 0.006
29 PiPE23 (45) 1 : 0.995 0.005
30 PiPE24 (45) 1 : 0.995 0.005
31 PiPE25 (45) 1 : 0.995 0.005
32 PiPE26 (50) 1 : 0.021 0.979
33 PiPE27 (45) 1 : 0.993 0.007
34 PiPE3 (47) 1 : 0.035 0.965
35 PiPE4 (47) 1 : 0.007 0.993
36 PiPE5 (47) 1 : 0.006 0.994
37 PiPE6 (50) 1 : 0.047 0.953
38 PiPE7 (50) 1 : 0.016 0.984
39 PiPE8 (47) 1 : 0.010 0.990
40 PiPE9 (50) 1 : 0.006 0.994
Estimated Allele Frequencies in each cluster
First column gives estimated ancestral frequencies
Locus 1 :
5 alleles
49.4% missing data
162 (0.179) 0.062 0.803
160 (0.595) 0.840 0.165
158 (0.076) 0.039 0.004
154 (0.075) 0.039 0.004
164 (0.075) 0.019 0.023
Locus 2 :
13 alleles
46.9% missing data
136 (0.141) 0.159 0.414
132 (0.050) 0.012 0.041
108 (0.078) 0.118 0.010
112 (0.049) 0.022 0.011
134 (0.081) 0.040 0.120
138 (0.074) 0.146 0.004
142 (0.133) 0.205 0.100
144 (0.092) 0.111 0.021
146 (0.083) 0.068 0.038
118 (0.054) 0.013 0.099
154 (0.056) 0.014 0.118
140 (0.062) 0.079 0.003
152 (0.048) 0.013 0.021
Locus 3 :
1 alleles
50.0% missing data
203 (1.000) 1.000 1.000
Locus 4 :
4 alleles
50.0% missing data
166 (0.377) 0.404 0.389
170 (0.454) 0.556 0.392
160 (0.084) 0.020 0.109
168 (0.085) 0.020 0.109
Locus 5 :
10 alleles
41.2% missing data
205 (0.071) 0.017 0.276
213 (0.260) 0.393 0.312
217 (0.214) 0.253 0.367
225 (0.054) 0.023 0.010
221 (0.073) 0.077 0.003
251 (0.056) 0.033 0.003
255 (0.065) 0.055 0.003
209 (0.073) 0.077 0.003
267 (0.054) 0.032 0.003
215 (0.080) 0.039 0.020
Locus 6 :
3 alleles
50.0% missing data
178 (0.592) 0.582 0.889
174 (0.075) 0.029 0.014
176 (0.333) 0.390 0.097
Locus 7 :
15 alleles
43.8% missing data
156 (0.095) 0.035 0.644
152 (0.102) 0.220 0.006
200 (0.112) 0.276 0.006
162 (0.082) 0.143 0.005
130 (0.059) 0.048 0.003
164 (0.056) 0.048 0.003
150 (0.048) 0.028 0.003
204 (0.050) 0.028 0.003
160 (0.081) 0.055 0.022
140 (0.055) 0.011 0.106
148 (0.056) 0.012 0.106
166 (0.056) 0.012 0.085
154 (0.048) 0.028 0.003
198 (0.049) 0.028 0.003
170 (0.050) 0.028 0.003
Locus 8 :
2 alleles
50.0% missing data
174 (0.224) 0.117 0.391
176 (0.776) 0.883 0.609
Locus 9 :
3 alleles
41.9% missing data
157 (0.497) 0.319 0.972
148 (0.234) 0.303 0.013
151 (0.270) 0.379 0.015
Locus 10 :
3 alleles
50.0% missing data
192 (0.680) 0.636 0.900
189 (0.225) 0.340 0.013
195 (0.094) 0.024 0.087
Locus 11 :
2 alleles
51.2% missing data
179 (0.708) 0.830 0.386
181 (0.292) 0.170 0.614
Values of parameters used in structure:
DATAFILE=/Users/maleja/Desktop/Structure/SA/SA/project_data, OUTFILE=/Users/maleja/Desktop/Structure/SA/SA/New/Results/New_run_19, NUMINDS=40, NUMLOCI=11, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=2, 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=1370296738,
[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,