| 1 | parameter file: rgEigPCAtest1_pca.xls.par |
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| 2 | ### THE INPUT PARAMETERS |
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| 3 | ##PARAMETER NAME: VALUE |
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| 4 | genotypename: /opt/galaxy/test-data/tinywga.bed |
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| 5 | snpname: /opt/galaxy/test-data/tinywga.bim |
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| 6 | indivname: /opt/galaxy/test-data/tinywga.fam |
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| 7 | evecoutname: rgEigPCAtest1_pca.xls.evec |
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| 8 | evaloutname: rgEigPCAtest1_eval.xls |
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| 9 | altnormstyle: NO |
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| 10 | numoutevec: 4 |
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| 11 | numoutlieriter: 2 |
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| 12 | numoutlierevec: 2 |
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| 13 | outliersigmathresh: 2 |
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| 14 | qtmode: 0 |
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| 15 | ## smartpca version: 8000 |
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| 16 | norm used |
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| 17 | |
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| 18 | genetic distance set from physical distance |
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| 19 | genotype file processed |
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| 20 | number of samples used: 40 number of snps used: 25 |
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| 21 | REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329 |
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| 22 | number of samples after outlier removal: 39 |
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| 23 | |
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| 24 | ## Tracy-Widom statistics: rows: 39 cols: 24 |
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| 25 | #N eigenvalue difference twstat p-value effect. n |
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| 26 | 1 11.481974 NA -0.712 0.332198 8.854 |
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| 27 | 2 7.739771 -3.742203 -1.302 0.510496 8.388 |
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| 28 | 3 7.254586 -0.485185 -0.171 0.201072 7.095 |
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| 29 | 4 4.270950 -2.983636 -0.191 0.205302 8.005 |
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| 30 | 5 2.538320 -1.732630 -0.341 0.238117 9.118 |
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| 31 | 6 1.667964 -0.870356 -0.231 0.21376 9.910 |
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| 32 | 7 1.043403 -0.624560 -0.269 0.222042 11.590 |
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| 33 | 8 0.653401 -0.390003 NA NA NA |
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| 34 | 9 0.391044 -0.262357 NA NA NA |
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| 35 | 10 0.338164 -0.052880 NA NA NA |
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| 36 | 11 0.263384 -0.074780 NA NA NA |
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| 37 | 12 0.150750 -0.112634 NA NA NA |
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| 38 | 13 0.085580 -0.065170 NA NA NA |
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| 39 | 14 0.065301 -0.020279 NA NA NA |
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| 40 | 15 0.048797 -0.016504 NA NA NA |
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| 41 | 16 0.006611 -0.042186 NA NA NA |
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| 42 | kurtosis snps indivs |
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| 43 | eigenvector 1 1.926 2.122 |
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| 44 | eigenvector 2 2.599 2.148 |
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| 45 | eigenvector 3 2.593 2.873 |
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| 46 | eigenvector 4 3.165 2.831 |
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| 47 | population: 0 Case 9 |
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| 48 | population: 1 Control 30 |
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| 49 | |
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| 50 | ## Average divergence between populations: |
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| 51 | Case Control popsize |
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| 52 | Case 1.028 0.954 9 |
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| 53 | Control 0.954 0.972 30 |
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| 54 | |
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| 55 | |
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| 56 | number of blocks for moving block jackknife: 1 |
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| 57 | fst *1000: |
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| 58 | C C |
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| 59 | C 0 0 |
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| 60 | C 0 0 |
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| 61 | |
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| 62 | s.dev * 1000000: |
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| 63 | C C |
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| 64 | C 0 0 |
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| 65 | C 0 0 |
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| 66 | |
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| 67 | ## Anova statistics for population differences along each eigenvector: |
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| 68 | p-value |
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| 69 | eigenvector_1_Case_Control_ 0.841067 |
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| 70 | eigenvector_2_Case_Control_ 0.758376 |
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| 71 | eigenvector_3_Case_Control_ 0.238793 |
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| 72 | eigenvector_4_Case_Control_ 0.678458 |
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| 73 | |
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| 74 | ## Statistical significance of differences beween populations: |
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| 75 | pop1 pop2 chisq p-value |pop1| |pop2| |
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| 76 | popdifference: Case Control 1.810 0.77061 9 30 |
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| 77 | |
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| 78 | eigbestsnp 1 rs762601 22 21898858 1.674 |
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| 79 | eigbestsnp 1 rs2156921 22 21899063 1.674 |
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| 80 | eigbestsnp 1 rs4822375 22 21905642 1.674 |
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| 81 | eigbestsnp 1 rs5751611 22 21896019 1.635 |
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| 82 | eigbestsnp 1 rs4820537 22 21794810 1.542 |
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| 83 | eigbestsnp 1 rs3788347 22 21797804 1.413 |
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| 84 | eigbestsnp 1 rs2267000 22 21785366 1.151 |
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| 85 | eigbestsnp 1 rs4820539 22 21807970 1.141 |
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| 86 | eigbestsnp 1 rs5751592 22 21827674 0.890 |
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| 87 | eigbestsnp 1 rs2283804 22 21820335 0.815 |
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| 88 | eigbestsnp 1 rs2267006 22 21820990 0.815 |
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| 89 | eigbestsnp 2 rs5759608 22 21832708 2.197 |
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| 90 | eigbestsnp 2 rs5759612 22 21833170 2.197 |
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| 91 | eigbestsnp 2 rs2283804 22 21820335 1.643 |
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| 92 | eigbestsnp 2 rs2267006 22 21820990 1.643 |
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| 93 | eigbestsnp 2 rs2283802 22 21784722 1.283 |
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| 94 | eigbestsnp 2 rs2267009 22 21860168 1.283 |
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| 95 | eigbestsnp 2 rs2071436 22 21871488 1.283 |
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| 96 | eigbestsnp 2 rs756632 22 21799918 0.942 |
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| 97 | eigbestsnp 2 rs16997606 22 21794754 0.715 |
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| 98 | eigbestsnp 2 rs6003566 22 21889806 0.645 |
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| 99 | eigbestsnp 2 rs762601 22 21898858 0.545 |
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| 100 | eigbestsnp 3 rs16997606 22 21794754 1.770 |
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| 101 | eigbestsnp 3 rs6003566 22 21889806 1.725 |
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| 102 | eigbestsnp 3 rs3788347 22 21797804 1.452 |
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| 103 | eigbestsnp 3 rs2267000 22 21785366 1.386 |
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| 104 | eigbestsnp 3 rs2283802 22 21784722 1.247 |
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| 105 | eigbestsnp 3 rs2267009 22 21860168 1.247 |
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| 106 | eigbestsnp 3 rs2071436 22 21871488 1.247 |
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| 107 | eigbestsnp 3 rs4820537 22 21794810 1.168 |
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| 108 | eigbestsnp 3 rs762601 22 21898858 1.153 |
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| 109 | eigbestsnp 3 rs2156921 22 21899063 1.153 |
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| 110 | eigbestsnp 3 rs4822375 22 21905642 1.153 |
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| 111 | eigbestsnp 4 rs756632 22 21799918 2.146 |
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| 112 | eigbestsnp 4 rs4820539 22 21807970 1.938 |
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| 113 | eigbestsnp 4 rs2267013 22 21875879 1.917 |
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| 114 | eigbestsnp 4 rs2256725 22 21892891 1.917 |
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| 115 | eigbestsnp 4 rs2283804 22 21820335 1.336 |
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| 116 | eigbestsnp 4 rs2267006 22 21820990 1.336 |
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| 117 | eigbestsnp 4 rs6003566 22 21889806 1.000 |
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| 118 | eigbestsnp 4 rs16997606 22 21794754 0.875 |
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| 119 | eigbestsnp 4 rs5751611 22 21896019 0.823 |
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| 120 | eigbestsnp 4 rs5759636 22 21868698 0.799 |
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| 121 | eigbestsnp 4 rs2267000 22 21785366 0.584 |
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| 122 | packedancestrymap output |
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| 123 | ##end of smartpca run |
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| 124 | |
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| 125 | Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033 |
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| 126 | Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051 |
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| 127 | Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 |
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| 128 | Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069 |
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