parameter file: rgEigPCAtest1_pca.xls.par ### THE INPUT PARAMETERS ##PARAMETER NAME: VALUE genotypename: /opt/galaxy/test-data/tinywga.bed snpname: /opt/galaxy/test-data/tinywga.bim indivname: /opt/galaxy/test-data/tinywga.fam evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO numoutevec: 4 numoutlieriter: 2 numoutlierevec: 2 outliersigmathresh: 2 qtmode: 0 ## smartpca version: 8000 norm used genetic distance set from physical distance genotype file processed number of samples used: 40 number of snps used: 25 REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329 number of samples after outlier removal: 39 ## Tracy-Widom statistics: rows: 39 cols: 24 #N eigenvalue difference twstat p-value effect. n 1 11.481974 NA -0.712 0.332198 8.854 2 7.739771 -3.742203 -1.302 0.510496 8.388 3 7.254586 -0.485185 -0.171 0.201072 7.095 4 4.270950 -2.983636 -0.191 0.205302 8.005 5 2.538320 -1.732630 -0.341 0.238117 9.118 6 1.667964 -0.870356 -0.231 0.21376 9.910 7 1.043403 -0.624560 -0.269 0.222042 11.590 8 0.653401 -0.390003 NA NA NA 9 0.391044 -0.262357 NA NA NA 10 0.338164 -0.052880 NA NA NA 11 0.263384 -0.074780 NA NA NA 12 0.150750 -0.112634 NA NA NA 13 0.085580 -0.065170 NA NA NA 14 0.065301 -0.020279 NA NA NA 15 0.048797 -0.016504 NA NA NA 16 0.006611 -0.042186 NA NA NA kurtosis snps indivs eigenvector 1 1.926 2.122 eigenvector 2 2.599 2.148 eigenvector 3 2.593 2.873 eigenvector 4 3.165 2.831 population: 0 Case 9 population: 1 Control 30 ## Average divergence between populations: Case Control popsize Case 1.028 0.954 9 Control 0.954 0.972 30 number of blocks for moving block jackknife: 1 fst *1000: C C C 0 0 C 0 0 s.dev * 1000000: C C C 0 0 C 0 0 ## Anova statistics for population differences along each eigenvector: p-value eigenvector_1_Case_Control_ 0.841067 eigenvector_2_Case_Control_ 0.758376 eigenvector_3_Case_Control_ 0.238793 eigenvector_4_Case_Control_ 0.678458 ## Statistical significance of differences beween populations: pop1 pop2 chisq p-value |pop1| |pop2| popdifference: Case Control 1.810 0.77061 9 30 eigbestsnp 1 rs762601 22 21898858 1.674 eigbestsnp 1 rs2156921 22 21899063 1.674 eigbestsnp 1 rs4822375 22 21905642 1.674 eigbestsnp 1 rs5751611 22 21896019 1.635 eigbestsnp 1 rs4820537 22 21794810 1.542 eigbestsnp 1 rs3788347 22 21797804 1.413 eigbestsnp 1 rs2267000 22 21785366 1.151 eigbestsnp 1 rs4820539 22 21807970 1.141 eigbestsnp 1 rs5751592 22 21827674 0.890 eigbestsnp 1 rs2283804 22 21820335 0.815 eigbestsnp 1 rs2267006 22 21820990 0.815 eigbestsnp 2 rs5759608 22 21832708 2.197 eigbestsnp 2 rs5759612 22 21833170 2.197 eigbestsnp 2 rs2283804 22 21820335 1.643 eigbestsnp 2 rs2267006 22 21820990 1.643 eigbestsnp 2 rs2283802 22 21784722 1.283 eigbestsnp 2 rs2267009 22 21860168 1.283 eigbestsnp 2 rs2071436 22 21871488 1.283 eigbestsnp 2 rs756632 22 21799918 0.942 eigbestsnp 2 rs16997606 22 21794754 0.715 eigbestsnp 2 rs6003566 22 21889806 0.645 eigbestsnp 2 rs762601 22 21898858 0.545 eigbestsnp 3 rs16997606 22 21794754 1.770 eigbestsnp 3 rs6003566 22 21889806 1.725 eigbestsnp 3 rs3788347 22 21797804 1.452 eigbestsnp 3 rs2267000 22 21785366 1.386 eigbestsnp 3 rs2283802 22 21784722 1.247 eigbestsnp 3 rs2267009 22 21860168 1.247 eigbestsnp 3 rs2071436 22 21871488 1.247 eigbestsnp 3 rs4820537 22 21794810 1.168 eigbestsnp 3 rs762601 22 21898858 1.153 eigbestsnp 3 rs2156921 22 21899063 1.153 eigbestsnp 3 rs4822375 22 21905642 1.153 eigbestsnp 4 rs756632 22 21799918 2.146 eigbestsnp 4 rs4820539 22 21807970 1.938 eigbestsnp 4 rs2267013 22 21875879 1.917 eigbestsnp 4 rs2256725 22 21892891 1.917 eigbestsnp 4 rs2283804 22 21820335 1.336 eigbestsnp 4 rs2267006 22 21820990 1.336 eigbestsnp 4 rs6003566 22 21889806 1.000 eigbestsnp 4 rs16997606 22 21794754 0.875 eigbestsnp 4 rs5751611 22 21896019 0.823 eigbestsnp 4 rs5759636 22 21868698 0.799 eigbestsnp 4 rs2267000 22 21785366 0.584 packedancestrymap output ##end of smartpca run Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033 Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051 Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069