act.out
Output for each iteration
Here t_mean is average or M for the autosomes, tx_mean is the average t or M for the X chromosome, t_corr is
l_mean is average l for the autosomes, lx_mean is the average l for the X chromosome, l_corr is
tau(A) is the African t, and tau(C) is the European t value, log score
Iter_Num t_mean tx_mean t_corr l_mean lx_mean l_corr tau(A) tau(B) log score
-99 0.201 0.181 0.878 5.941 6.238 0.025 100.000 100.000 4.057 0.000
-98 0.201 0.181 0.881 5.930 6.298 0.030 104.451 330.940 3.927 0.000
-97 0.201 0.179 0.875 5.935 6.142 0.000 136.273 218.875 5.307 0.000
-96 0.201 0.177 0.860 5.941 6.102 0.058 127.126 171.340 6.187 0.000
-95 0.200 0.175 0.843 5.850 6.117 0.015 94.072 125.312 6.175 0.000
-94 0.198 0.176 0.833 5.872 6.220 0.053 97.022 105.920 5.588 0.000
-93 0.198 0.176 0.837 5.848 6.031 0.032 91.925 92.764 6.530 0.000
-92 0.198 0.179 0.834 5.873 5.840 0.029 96.560 90.360 7.145 0.000
197 0.198 0.185 0.933 6.046 4.432 0.066 96.851 80.848 7.183 8.170
198 0.199 0.191 0.928 6.027 4.468 0.034 99.158 82.527 7.686 8.169
199 0.199 0.190 0.930 6.064 4.409 0.012 104.487 89.506 7.516 8.167
200 0.199 0.193 0.930 6.045 4.331 0.029 91.103 81.868 7.030 8.165
ethnic.out
For all the markers averaged over all the iterations and samples:
SNP_Index is the marker’s internal index number
SNP_Index SNP_ID Chr_Num Avg_Ethnicity
0 rs897634 1 0.212
1 fake-1:0 1 0.212
2 rs905135 1 0.212
3 fake-1:1 1 0.212
4748 rs2027812 23 0.180
4749 fake-23:3578 23 0.180
4750 fake-23:3579 23 0.179
4751 rs12557310 23 0.179
freq.out
For all the markers averaged over all the iterations and the samples:
SNP_Index is the marker’s internal Index number, anaive and bnaive are the naïve African and European frequencies, amean and bmean are the calculated African and European frequencies, asdev and bsdev are the corresponding standard deviation
SNP_Index SNP_ID Chr_Num anaive amean asdev bnaive bmean bsdev
0 rs897634 1 0.104 0.148 0.010 0.741 0.766 0.030
2 rs905135 1 0.333 0.240 0.012 0.934 0.917 0.025
7 rs12071910 1 0.398 0.374 0.014 0.927 0.939 0.020
12 rs1534997 1 0.806 0.747 0.011 0.100 0.045 0.013
14 rs3007429 1 0.500 0.593 0.013 0.041 0.027 0.013
4744 rs760109 23 0.013 0.019 0.004 0.448 0.466 0.028
4748 rs2027812 23 0.175 0.152 0.011 0.639 0.602 0.030
4751 rs12557310 23 0.955 0.994 0.004 0.258 0.311 0.036
ind.out
For all the individuals
Indiv_Id Gender Status Num_valid_genotypes
toyindiv:0 M Control 1252
toyindiv:1 F Control 1252
toyindiv:2 M Case 1252
toyindiv:3 F Case 1252
toyindiv:4 M Control 1252
….
toyindiv:997 F Control 1252
toyindiv:998 M Case 1252
toyindiv:999 F Case 1252
lambda.out
For all the individuals averaged over all the iterations
Here Indiv_Index is the individual’s internal index number, λ mean and λx mean are the average λ for the autosomes and the X chromosome,
λ sdev and λx sdev are the corresponding standard deviation
Indiv_Index Indiv_Id lam_mean lam_sdev lamX_mean lamX_sdev
0 toyindiv:0 6.172 0.901 4.045 1.519
1 toyindiv:1 7.368 1.090 5.604 1.858
2 toyindiv:2 6.421 1.107 4.377 1.438
snp.out
For all the markers:
###DETAILS ABOUT THE MARKERS
##Gen_Pos: genetic position, Phys_pos: Physical position
##Afr_vart: Parental African variant allele count, Afr_ref: Parental African reference allele count
##Eur_vart: Parental European variant allele count, Eur:ref:Parental European reference allele count
SNP_Id Chr_Num Gen_Pos Phys_Pos Afr_vart Afr_ref Eur_vart Eur_ref
rs897634 1 0.093937 2858849 22 190 243 85
rs905135 1 0.105907 3222641 36 72 282 20
rs12071910 1 0.148204 4620948 43 65 278 22
rs1534997 1 0.186068 6177981 87 21 30 270
theta.out
For all the individuals averaged over all the iterations:
Th_mean and thX_mean are the average M for the autosomes and X chromosome, th_sdev and thX_sdev are the corresponding standard deviation
Indiv_Index Indiv_Id th_mean th_sdev thX_mean thX_sdev Status
0 toyindiv:0 0.344 0.032 0.297 0.061 Control
1 toyindiv:1 0.140 0.022 0.144 0.043 Control
2 toyindiv:2 0.096 0.019 0.119 0.042 Case
3 toyindiv:3 0.091 0.019 0.090 0.034 Case