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SA_No_ADM_run_6_f
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SA_No_ADM_run_6_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/No_ADM/mainparams" -e "/Users/maleja/Desktop/Structure/SA/SA/No_ADM/extraparams"
Input File: /Users/maleja/Desktop/Structure/SA/SA/project_data
Run parameters:
40 individuals
11 loci
2 populations assumed
2500 Burn-in period
10000 Reps
NO ADMIXTURE model assumed
--------------------------------------------
Proportion of membership of each pre-defined
population in each of the 2 clusters
Given Inferred Clusters Number of
Pop 1 2 Individuals
1: 0.574 0.426 40
--------------------------------------------
Allele-freq. divergence among pops (Net nucleotide distance),
computed using point estimates of P.
1 2
1 - 0.1492
2 0.1492 -
Average distances (expected heterozygosity) between individuals in same cluster:
cluster 1 : 0.4084
cluster 2 : 0.4895
--------------------------------------------
Estimated Ln Prob of Data = -821.5
Mean value of ln likelihood = -797.1
Variance of ln likelihood = 48.8
Mean value of Fst_1 = 0.2401
Mean value of Fst_2 = 0.1075
Inferred ancestry of individuals:
Label (%Miss) Pop: Inferred clusters
1 PiCO1 (47) 1 : 1.000 0.000
2 PiCO2 (47) 1 : 1.000 0.000
3 PiCO3 (47) 1 : 1.000 0.000
4 PiCO4 (47) 1 : 1.000 0.000
5 PiCO5 (50) 1 : 0.965 0.035
6 PiEC1 (50) 1 : 1.000 0.000
7 PiEC10 (47) 1 : 0.000 1.000
8 PiEC11 (47) 1 : 0.000 1.000
9 PiEC12 (47) 1 : 0.000 1.000
10 PiEC13 (45) 1 : 0.000 1.000
11 PiEC14 (45) 1 : 0.000 1.000
12 PiEC2 (47) 1 : 1.000 0.000
13 PiEC3 (50) 1 : 1.000 0.000
14 PiEC4 (47) 1 : 0.000 1.000
15 PiEC5 (52) 1 : 0.000 1.000
16 PiEC6 (43) 1 : 0.000 1.000
17 PiEC7 (50) 1 : 0.000 1.000
18 PiEC8 (50) 1 : 0.000 1.000
19 PiPE1 (47) 1 : 1.000 0.000
20 PiPE10 (50) 1 : 1.000 0.000
21 PiPE11 (47) 1 : 1.000 0.000
22 PiPE12 (47) 1 : 1.000 0.000
23 PiPE13 (45) 1 : 1.000 0.000
24 PiPE14 (47) 1 : 1.000 0.000
25 PiPE2 (47) 1 : 1.000 0.000
26 PiPE20 (43) 1 : 0.000 1.000
27 PiPE21 (45) 1 : 0.000 1.000
28 PiPE22 (45) 1 : 0.000 1.000
29 PiPE23 (45) 1 : 0.000 1.000
30 PiPE24 (45) 1 : 0.000 1.000
31 PiPE25 (45) 1 : 0.000 1.000
32 PiPE26 (50) 1 : 1.000 0.000
33 PiPE27 (45) 1 : 0.000 1.000
34 PiPE3 (47) 1 : 1.000 0.000
35 PiPE4 (47) 1 : 1.000 0.000
36 PiPE5 (47) 1 : 1.000 0.000
37 PiPE6 (50) 1 : 1.000 0.000
38 PiPE7 (50) 1 : 1.000 0.000
39 PiPE8 (47) 1 : 1.000 0.000
40 PiPE9 (50) 1 : 1.000 0.000
Estimated Allele Frequencies in each cluster
First column gives estimated ancestral frequencies
Locus 1 :
5 alleles
49.4% missing data
162 (0.209) 0.786 0.065
160 (0.563) 0.179 0.844
158 (0.075) 0.005 0.037
154 (0.076) 0.005 0.038
164 (0.076) 0.025 0.015
Locus 2 :
13 alleles
46.9% missing data
136 (0.139) 0.396 0.168
132 (0.053) 0.040 0.011
108 (0.091) 0.024 0.112
112 (0.049) 0.021 0.011
134 (0.087) 0.116 0.042
138 (0.071) 0.004 0.154
142 (0.120) 0.099 0.212
144 (0.091) 0.024 0.112
146 (0.084) 0.042 0.063
118 (0.051) 0.095 0.011
154 (0.057) 0.115 0.012
140 (0.060) 0.004 0.082
152 (0.048) 0.021 0.010
Locus 3 :
1 alleles
50.0% missing data
203 (1.000) 1.000 1.000
Locus 4 :
4 alleles
50.0% missing data
166 (0.374) 0.389 0.405
170 (0.451) 0.395 0.559
160 (0.085) 0.108 0.017
168 (0.090) 0.107 0.018
Locus 5 :
10 alleles
41.2% missing data
205 (0.074) 0.269 0.014
213 (0.264) 0.313 0.400
217 (0.205) 0.360 0.257
225 (0.056) 0.020 0.012
221 (0.067) 0.004 0.078
251 (0.056) 0.003 0.032
255 (0.065) 0.004 0.056
209 (0.071) 0.004 0.080
267 (0.057) 0.003 0.033
215 (0.084) 0.021 0.037
Locus 6 :
3 alleles
50.0% missing data
178 (0.608) 0.874 0.592
174 (0.078) 0.025 0.017
176 (0.314) 0.101 0.391
Locus 7 :
15 alleles
43.8% missing data
156 (0.110) 0.635 0.039
152 (0.086) 0.006 0.223
200 (0.095) 0.006 0.280
162 (0.077) 0.005 0.145
130 (0.061) 0.004 0.048
164 (0.059) 0.004 0.048
150 (0.044) 0.003 0.026
204 (0.051) 0.004 0.028
160 (0.091) 0.027 0.053
140 (0.061) 0.106 0.010
148 (0.057) 0.105 0.010
166 (0.064) 0.085 0.011
154 (0.050) 0.003 0.027
198 (0.052) 0.003 0.027
170 (0.044) 0.003 0.026
Locus 8 :
2 alleles
50.0% missing data
174 (0.245) 0.382 0.119
176 (0.755) 0.618 0.881
Locus 9 :
3 alleles
41.9% missing data
157 (0.543) 0.970 0.320
148 (0.216) 0.014 0.303
151 (0.241) 0.016 0.377
Locus 10 :
3 alleles
50.0% missing data
192 (0.703) 0.899 0.636
189 (0.202) 0.013 0.344
195 (0.095) 0.088 0.019
Locus 11 :
2 alleles
51.2% missing data
179 (0.683) 0.392 0.833
181 (0.317) 0.608 0.167
Values of parameters used in structure:
DATAFILE=/Users/maleja/Desktop/Structure/SA/SA/project_data, OUTFILE=/Users/maleja/Desktop/Structure/SA/SA/No_ADM/Results/No_ADM_run_6, NUMINDS=40, NUMLOCI=11, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=2, BURNIN=2500, NUMREPS=10000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=1, ADMBURNIN=1250, 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=0.0500, 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=1370631013,
[STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,