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| author | iuc |
|---|---|
| date | Wed, 25 Sep 2024 15:36:50 +0000 |
| parents | 8a7390c4d6bf |
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---------------------------------------------------- STRUCTURE by Pritchard, Stephens and Donnelly (2000) Code by J.K. Pritchard Modified by Daniel Falush to incorporate recombination breakpoints Version 2.0 (July 2001) ---------------------------------------------------- Command line arguments: bin/structure.exe -m \mainparams -e \extraparams Input File: \project_data Run parameters: 95 individuals 18 loci 2 populations assumed 50000 Burn-in period 500000 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: 0.001 0.999 6 2: 0.002 0.998 6 3: 0.001 0.999 6 4: 0.002 0.998 6 5: 0.002 0.998 6 6: 0.003 0.997 6 7: 0.001 0.999 6 8: 0.001 0.999 6 9: 0.002 0.998 6 10: 0.005 0.995 6 11: 0.001 0.999 6 12: 0.002 0.998 6 13: 0.002 0.998 6 14: 0.002 0.998 6 15: 0.999 0.001 6 16: 0.998 0.002 5 -------------------------------------------- Allele-freq. divergence among pops (Kullback-Leibler distance), computed using point estimates of P. 1 2 1 - 2.67 2 2.10 - -------------------------------------------- Estimated Ln Prob of Data = -3646.5 Mean value of ln likelihood = -3597.1 Variance of ln likelihood = 98.8 Mean value of alpha = 0.0254 Mean value of Fst_1 = 0.5120 Mean value of Fst_2 = 0.0523 Inferred ancestry of individuals: Label (%Miss) Pop: Inferred clusters 1 A01 (0) 1 : 0.001 0.999 2 A02 (0) 1 : 0.002 0.998 3 A03 (0) 1 : 0.001 0.999 4 A04 (0) 1 : 0.001 0.999 5 A05 (0) 1 : 0.002 0.998 6 A24 (0) 1 : 0.001 0.999 7 B466 (0) 2 : 0.001 0.999 8 B479 (0) 2 : 0.001 0.999 9 B480 (0) 2 : 0.001 0.999 10 B482 (0) 2 : 0.002 0.998 11 B484 (0) 2 : 0.003 0.997 12 B485 (0) 2 : 0.001 0.999 13 C02 (0) 3 : 0.001 0.999 14 C05 (0) 3 : 0.001 0.999 15 C14 (0) 3 : 0.001 0.999 16 C30 (0) 3 : 0.001 0.999 17 C31 (0) 3 : 0.001 0.999 18 C40 (0) 3 : 0.001 0.999 19 D08 (0) 4 : 0.002 0.998 20 D09 (0) 4 : 0.001 0.999 21 D13 (0) 4 : 0.003 0.997 22 D21 (0) 4 : 0.002 0.998 23 D25 (0) 4 : 0.001 0.999 24 D30 (0) 4 : 0.001 0.999 25 E01 (0) 5 : 0.003 0.997 26 E02 (0) 5 : 0.003 0.997 27 E03 (0) 5 : 0.001 0.999 28 E04 (0) 5 : 0.002 0.998 29 E05 (0) 5 : 0.002 0.998 30 E06 (0) 5 : 0.002 0.998 31 F03 (0) 6 : 0.010 0.990 32 F05 (0) 6 : 0.001 0.999 33 F08 (0) 6 : 0.002 0.998 34 F14 (0) 6 : 0.001 0.999 35 F25 (0) 6 : 0.001 0.999 36 F35 (0) 6 : 0.001 0.999 37 B360 (0) 7 : 0.001 0.999 38 B365 (0) 7 : 0.001 0.999 39 B367 (0) 7 : 0.001 0.999 40 B370 (0) 7 : 0.001 0.999 41 B371 (0) 7 : 0.001 0.999 42 B372 (0) 7 : 0.001 0.999 43 B341 (0) 8 : 0.002 0.998 44 B342 (0) 8 : 0.001 0.999 45 B343 (0) 8 : 0.001 0.999 46 B345 (0) 8 : 0.001 0.999 47 B346 (0) 8 : 0.001 0.999 48 B349 (0) 8 : 0.001 0.999 49 B121 (0) 9 : 0.002 0.998 50 B122 (0) 9 : 0.001 0.999 51 B125 (0) 9 : 0.003 0.997 52 B127 (0) 9 : 0.001 0.999 53 B128 (0) 9 : 0.002 0.998 54 B129 (0) 9 : 0.003 0.997 55 B306 (0) 10 : 0.016 0.984 56 B310 (0) 10 : 0.001 0.999 57 B312 (0) 10 : 0.002 0.998 58 B313 (0) 10 : 0.004 0.996 59 B317 (0) 10 : 0.001 0.999 60 B318 (0) 10 : 0.005 0.995 61 G19 (0) 11 : 0.001 0.999 62 G20 (0) 11 : 0.001 0.999 63 G21 (0) 11 : 0.001 0.999 64 G22 (0) 11 : 0.001 0.999 65 G23 (0) 11 : 0.002 0.998 66 G24 (0) 11 : 0.001 0.999 67 H01 (0) 12 : 0.001 0.999 68 H02 (0) 12 : 0.002 0.998 69 H03 (0) 12 : 0.001 0.999 70 H04 (0) 12 : 0.002 0.998 71 H05 (0) 12 : 0.002 0.998 72 H12 (0) 12 : 0.002 0.998 73 I20 (0) 13 : 0.002 0.998 74 I21 (0) 13 : 0.001 0.999 75 I23 (0) 13 : 0.002 0.998 76 I24 (0) 13 : 0.002 0.998 77 I25 (0) 13 : 0.002 0.998 78 I26 (0) 13 : 0.002 0.998 79 J02 (0) 14 : 0.002 0.998 80 J04 (0) 14 : 0.001 0.999 81 J05 (0) 14 : 0.001 0.999 82 J08 (0) 14 : 0.001 0.999 83 J09 (0) 14 : 0.002 0.998 84 J10 (0) 14 : 0.001 0.999 85 K20 (5) 15 : 0.999 0.001 86 K33 (5) 15 : 0.999 0.001 87 K34 (5) 15 : 0.999 0.001 88 K35 (5) 15 : 0.999 0.001 89 K53 (5) 15 : 0.999 0.001 90 K56 (5) 15 : 0.999 0.001 91 L04 (5) 16 : 0.999 0.001 92 L07 (5) 16 : 0.999 0.001 93 L14 (5) 16 : 0.996 0.004 94 L26 (5) 16 : 0.999 0.001 95 L27 (5) 16 : 0.999 0.001 Estimated Allele Frequencies in each population First column gives estimated ancestral frequencies Locus 1 : L1 7 alleles 0.0% missing data 118 (0.478) 0.020 0.670 127 (0.104) 0.004 0.080 130 (0.081) 0.484 0.024 114 (0.069) 0.003 0.034 122 (0.119) 0.005 0.103 110 (0.107) 0.005 0.086 135 (0.042) 0.478 0.004 Locus 2 : L2 15 alleles 0.0% missing data 228 (0.091) 0.004 0.111 222 (0.099) 0.004 0.133 225 (0.119) 0.005 0.178 234 (0.043) 0.002 0.015 219 (0.111) 0.005 0.161 213 (0.147) 0.006 0.250 204 (0.037) 0.002 0.009 216 (0.058) 0.002 0.038 195 (0.042) 0.002 0.015 231 (0.052) 0.002 0.027 210 (0.051) 0.002 0.027 240 (0.037) 0.002 0.009 207 (0.047) 0.002 0.021 198 (0.034) 0.915 0.003 185 (0.033) 0.045 0.003 Locus 3 : L3 3 alleles 0.0% missing data 266 (0.873) 0.037 0.961 272 (0.079) 0.003 0.035 278 (0.048) 0.959 0.005 Locus 4 : L4 19 alleles 0.0% missing data 164 (0.081) 0.003 0.121 173 (0.146) 0.006 0.357 182 (0.066) 0.003 0.076 170 (0.043) 0.002 0.020 200 (0.043) 0.002 0.020 202 (0.034) 0.001 0.009 176 (0.033) 0.001 0.009 185 (0.045) 0.002 0.026 167 (0.054) 0.002 0.043 158 (0.067) 0.003 0.076 155 (0.049) 0.002 0.032 152 (0.061) 0.003 0.060 179 (0.033) 0.001 0.009 145 (0.034) 0.001 0.009 149 (0.061) 0.003 0.060 161 (0.063) 0.003 0.065 136 (0.031) 0.872 0.003 101 (0.029) 0.044 0.003 139 (0.029) 0.044 0.003 Locus 5 : L5 24 alleles 0.0% missing data 182 (0.060) 0.090 0.059 188 (0.040) 0.002 0.036 185 (0.052) 0.002 0.080 194 (0.038) 0.002 0.031 209 (0.028) 0.001 0.008 191 (0.038) 0.002 0.031 160 (0.055) 0.265 0.043 200 (0.036) 0.002 0.025 173 (0.061) 0.090 0.065 176 (0.036) 0.002 0.025 169 (0.036) 0.002 0.025 131 (0.028) 0.001 0.008 166 (0.040) 0.002 0.036 154 (0.045) 0.002 0.053 144 (0.054) 0.002 0.097 157 (0.044) 0.002 0.047 203 (0.032) 0.001 0.014 147 (0.044) 0.002 0.053 134 (0.063) 0.003 0.146 141 (0.047) 0.002 0.064 206 (0.036) 0.002 0.025 151 (0.035) 0.001 0.020 137 (0.028) 0.001 0.008 179 (0.024) 0.520 0.002 Locus 6 : L6 6 alleles 11.6% missing data 177 (0.168) 0.166 0.167 165 (0.156) 0.152 0.150 171 (0.346) 0.358 0.426 175 (0.165) 0.160 0.161 183 (0.086) 0.086 0.051 179 (0.080) 0.078 0.045 Locus 7 : L7 10 alleles 0.0% missing data 187 (0.202) 0.009 0.288 191 (0.125) 0.005 0.141 183 (0.185) 0.008 0.254 195 (0.105) 0.004 0.102 199 (0.063) 0.003 0.033 180 (0.063) 0.003 0.033 203 (0.071) 0.003 0.045 206 (0.078) 0.003 0.056 214 (0.070) 0.003 0.044 138 (0.039) 0.959 0.004 Locus 8 : L8 7 alleles 0.0% missing data 151 (0.466) 0.020 0.632 148 (0.084) 0.003 0.051 145 (0.059) 0.960 0.010 157 (0.044) 0.002 0.010 155 (0.109) 0.005 0.086 135 (0.064) 0.003 0.028 141 (0.174) 0.007 0.184 Locus 9 : L9 10 alleles 0.0% missing data 138 (0.241) 0.010 0.389 140 (0.065) 0.003 0.039 147 (0.137) 0.964 0.098 142 (0.126) 0.005 0.152 145 (0.098) 0.004 0.096 136 (0.061) 0.003 0.033 134 (0.047) 0.002 0.015 132 (0.052) 0.002 0.021 153 (0.112) 0.005 0.124 149 (0.061) 0.003 0.033 Locus 10 : L10 7 alleles 0.0% missing data 313 (0.102) 0.004 0.080 317 (0.368) 0.016 0.493 321 (0.073) 0.003 0.039 319 (0.109) 0.445 0.047 325 (0.044) 0.002 0.010 306 (0.262) 0.011 0.327 324 (0.042) 0.519 0.004 Locus 11 : L11 8 alleles 0.0% missing data 250 (0.219) 0.009 0.312 247 (0.083) 0.003 0.062 242 (0.100) 0.004 0.090 251 (0.072) 0.003 0.045 245 (0.113) 0.005 0.113 257 (0.049) 0.002 0.016 243 (0.262) 0.969 0.266 253 (0.104) 0.004 0.096 Locus 12 : L12 4 alleles 0.0% missing data 204 (0.823) 0.950 0.929 180 (0.053) 0.002 0.016 218 (0.085) 0.004 0.051 210 (0.040) 0.044 0.004 Locus 13 : L13 6 alleles 0.0% missing data 260 (0.696) 0.857 0.884 263 (0.111) 0.092 0.059 257 (0.050) 0.002 0.016 269 (0.061) 0.003 0.028 275 (0.043) 0.002 0.010 246 (0.038) 0.044 0.004 Locus 14 : L14 5 alleles 0.0% missing data 157 (0.640) 0.985 0.723 146 (0.187) 0.008 0.206 153 (0.057) 0.002 0.022 155 (0.073) 0.003 0.039 163 (0.043) 0.002 0.010 Locus 15 : L15 2 alleles 0.0% missing data 243 (0.639) 0.943 0.636 238 (0.361) 0.057 0.364 Locus 16 : L16 3 alleles 0.0% missing data 173 (0.788) 0.991 0.845 165 (0.077) 0.003 0.040 169 (0.135) 0.006 0.115 Locus 17 : L17 2 alleles 0.0% missing data 171 (0.951) 0.041 0.995 168 (0.049) 0.959 0.005 Locus 18 : L18 4 alleles 0.0% missing data 286 (0.764) 0.032 0.898 287 (0.108) 0.005 0.070 283 (0.064) 0.003 0.022 290 (0.064) 0.960 0.010 Values of parameters used in structure: DATAFILE=\project_data, OUTFILE=\Results_run_2, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=2, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=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=2, PHASEINFO=0 [STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,