Preprocessing


The original data included 41830521 CpG sites across all samples.


CpG sites from unplaced contigs were removed, leaving 41793082 CpG sites.

Multidimensional scaling (MDS) plot of raw methylation data.


Differential methylation analyses

Differential methylation analyses were conducted in DSS bioconductor package.


Comparison EM.24M vs EM.3M

Wald test was used.

Output files include the following:

  • mu1, mu2: group means

  • diff, diff.se: differece between group means and the standard error of differences

  • stat: hypothesis test statistics (Wald test)

  • phi1, phi2: dispersions

  • pvals: Raw p-value from test that the methylation difference differs from 0

  • fdrs: Benjamini-Hochberg false discovery rate (FDR) adjusted p-value


Smoothing ...
Estimating dispersion for each CpG site, this will take a while ...

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Computing test statistics ...


Top 500 Differential methylated CpG sites
Number of differentially methylated CpGs with FDR adjusted P < 0.05 = 5687
chr pos mu1 mu2 diff diff.se stat phi1 phi2 pval fdr postprob.overThreshold
chr1 44889389 0.9794731 0.5428014 0.4366717 0.0392964 11.112252 0.0296764 0.0247160 0e+00 0.0000000 1.0000000
chr1 68952683 0.4162853 0.9764757 -0.5601904 0.0457822 -12.235981 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr13 113771417 0.7046225 0.2757455 0.4288769 0.0367403 11.673197 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr2 130879980 0.5605775 0.9715961 -0.4110186 0.0336938 -12.198653 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr8 96087979 0.9083516 0.4887706 0.4195810 0.0370101 11.336918 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr8 118761682 0.8175145 0.4828273 0.3346872 0.0284317 11.771629 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr8 6972995 0.5517717 0.8720632 -0.3202915 0.0274203 -11.680808 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr16 19848500 0.9758134 0.3879215 0.5878919 0.0608844 9.655874 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr7 61210499 0.4510085 0.8614083 -0.4103998 0.0388510 -10.563437 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr3 45567526 0.8356363 0.4361483 0.3994880 0.0378609 10.551455 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr14 100603928 0.5153191 0.9431116 -0.4277925 0.0423247 -10.107386 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr15 33623838 0.9211261 0.5578024 0.3633238 0.0342670 10.602724 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrY 89544849 0.1702319 0.8701642 -0.6999323 0.0782369 -8.946319 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 49572111 0.4636704 0.9614952 -0.4978247 0.0520956 -9.555978 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr1 103274808 0.9775448 0.6244454 0.3530993 0.0336313 10.499136 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr1 117037801 0.5454059 0.9712856 -0.4258796 0.0433582 -9.822361 0.0274279 0.0247160 0e+00 0.0000000 1.0000000
chr6 60953418 0.9628450 0.4564993 0.5063457 0.0549083 9.221658 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 152929260 0.9634308 0.5330184 0.4304124 0.0451149 9.540367 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr5 18137559 0.6813046 0.2896974 0.3916072 0.0404015 9.692890 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrY 42431476 0.9742749 0.5091154 0.4651595 0.0507267 9.169916 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 65635944 0.9711078 0.5081599 0.4629479 0.0505534 9.157595 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr13 5969346 0.5977153 0.8835666 -0.2858513 0.0260922 -10.955428 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 153889055 0.3497835 0.9649406 -0.6151571 0.0723764 -8.499418 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr1 125499781 0.7160587 0.9755543 -0.2594956 0.0224915 -11.537493 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr5 9539412 0.6594682 0.9747528 -0.3152846 0.0308548 -10.218331 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr15 90019374 0.9720911 0.4637260 0.5083651 0.0596919 8.516479 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr17 16657308 0.8574378 0.2987597 0.5586781 0.0678832 8.229991 0.0276810 0.0253192 0e+00 0.0000000 1.0000000
chr15 46973667 0.9873790 0.6846819 0.3026971 0.0300994 10.056583 0.0298243 0.0247160 0e+00 0.0000000 1.0000000
chr3 127295463 0.7151266 0.1328661 0.5822605 0.0716332 8.128359 0.0276810 0.0247160 0e+00 0.0000000 1.0000000
chr13 66306065 0.4616184 0.8979929 -0.4363745 0.0499905 -8.729143 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr13 66306127 0.4616184 0.8979929 -0.4363745 0.0499905 -8.729143 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr4 114270578 0.2957850 0.8958804 -0.6000954 0.0750119 -7.999998 0.0368806 0.0248755 0e+00 0.0000000 1.0000000
chr10 23019369 0.9284061 0.5732900 0.3551161 0.0383428 9.261620 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr8 29808976 0.7735342 0.2890859 0.4844483 0.0582085 8.322635 0.0322371 0.0247160 0e+00 0.0000000 1.0000000
chr19 31772123 0.9685376 0.5873565 0.3811811 0.0427894 8.908299 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr3 20339724 0.6721222 0.9838617 -0.3117395 0.0323904 -9.624441 0.0295565 0.0247807 0e+00 0.0000000 1.0000000
chr15 71423093 0.6186429 0.9254003 -0.3067574 0.0319927 -9.588367 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr1 46794108 0.9251449 0.5138905 0.4112544 0.0483302 8.509270 0.0278066 0.0247160 0e+00 0.0000000 1.0000000
chr18 27705890 0.1351343 0.5979278 -0.4627935 0.0564829 -8.193512 0.0327647 0.0270367 0e+00 0.0000000 1.0000000
chr2 6839752 0.8123426 0.3292499 0.4830927 0.0598487 8.071905 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr8 18453425 0.6467117 0.9761998 -0.3294881 0.0359238 -9.171871 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr8 112941829 0.6154877 0.9735261 -0.3580384 0.0404062 -8.860969 0.0295565 0.0248297 0e+00 0.0000000 1.0000000
chr13 18935895 0.5105870 0.8910258 -0.3804388 0.0446003 -8.529963 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr18 76788275 0.3022042 0.9541593 -0.6519550 0.0880916 -7.400878 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr14 90110755 0.2570099 0.8634817 -0.6064718 0.0812543 -7.463870 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr5 9420235 0.7241938 0.2730746 0.4511193 0.0564356 7.993519 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr7 30053462 0.8853556 0.5889668 0.2963888 0.0317589 9.332459 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 53995057 0.9755900 0.3272878 0.6483022 0.0887269 7.306713 0.0296996 0.0254214 0e+00 0.0000001 1.0000000
chrY 8807114 0.9632802 0.2582820 0.7049982 0.0984297 7.162450 0.0297165 0.0247160 0e+00 0.0000001 1.0000000
chr19 26327203 0.9813966 0.6794073 0.3019892 0.0328750 9.185974 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 149677453 0.7299254 0.1715718 0.5583536 0.0750462 7.440135 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr12 10788782 0.5891547 0.9665574 -0.3774027 0.0455591 -8.283813 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 79891418 0.9248085 0.2957081 0.6291004 0.0874368 7.194916 0.0312523 0.0253352 0e+00 0.0000001 1.0000000
chr4 35232744 0.5783459 0.9673889 -0.3890430 0.0477910 -8.140514 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr16 40807491 0.6172765 0.9422285 -0.3249520 0.0373260 -8.705785 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr9 91079700 0.9663788 0.3480061 0.6183727 0.0861695 7.176239 0.0296285 0.0254587 0e+00 0.0000001 1.0000000
chr4 39312637 0.3585044 0.9570603 -0.5985559 0.0829188 -7.218581 0.0276810 0.0247823 0e+00 0.0000001 1.0000000
chr5 14925162 0.8848388 0.6433912 0.2414476 0.0236180 10.223050 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr15 69353795 0.8554950 0.3492380 0.5062570 0.0678638 7.459900 0.0295565 0.0247168 0e+00 0.0000000 1.0000000
GL456221.1 156267 0.8030903 0.3514708 0.4516196 0.0588439 7.674874 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr1 101697813 0.9769025 0.5273000 0.4496025 0.0585739 7.675820 0.0296909 0.0247160 0e+00 0.0000000 1.0000000
chr4 68689987 0.7740862 0.4389951 0.3350911 0.0394614 8.491618 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 49154321 0.5384062 0.9485955 -0.4101893 0.0522437 -7.851459 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr11 65513101 0.8434624 0.4059938 0.4374686 0.0569096 7.687075 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr14 6395510 0.4300565 0.8586225 -0.4285660 0.0554994 -7.721991 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr7 8290812 0.8799828 0.4611839 0.4187989 0.0539441 7.763567 0.0298384 0.0233895 0e+00 0.0000000 1.0000000
chrX 117086661 0.5563376 0.9715065 -0.4151689 0.0534326 -7.769954 0.0295565 0.0247579 0e+00 0.0000000 1.0000000
chr6 10002303 0.9229186 0.5735312 0.3493874 0.0422913 8.261456 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr9 104623305 0.9379300 0.6459189 0.2920112 0.0325824 8.962229 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr8 50305947 0.8410231 0.5056730 0.3353501 0.0399453 8.395231 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr6 10696261 0.8920365 0.4095185 0.4825179 0.0654132 7.376464 0.0276810 0.0247160 0e+00 0.0000000 1.0000000
chr5 129459748 0.9257134 0.5361174 0.3895960 0.0496281 7.850309 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr16 58243161 0.5143071 0.9612985 -0.4469914 0.0594909 -7.513609 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr6 69479683 0.3110766 0.8947265 -0.5836498 0.0829728 -7.034232 0.0233050 0.0207627 0e+00 0.0000003 1.0000000
JH584299.1 283909 0.9254874 0.6014464 0.3240409 0.0385353 8.408935 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 132483284 0.9626330 0.5136583 0.4489747 0.0600480 7.476933 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr6 109582256 0.5733775 0.0900967 0.4832809 0.0660274 7.319396 0.0301744 0.0248562 0e+00 0.0000001 1.0000000
chr7 59031217 0.8475829 0.2272309 0.6203520 0.0896702 6.918149 0.0295565 0.0233895 0e+00 0.0000006 1.0000000
chr17 42552546 0.4557682 0.9767149 -0.5209467 0.0726110 -7.174488 0.0295565 0.0248194 0e+00 0.0000001 1.0000000
chr5 126794153 0.6358685 0.9286795 -0.2928111 0.0333050 -8.791806 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr12 35633406 0.5058926 0.9215845 -0.4156919 0.0545495 -7.620447 0.0295565 0.0248369 0e+00 0.0000000 1.0000000
chrX 78317340 0.2236633 0.8579974 -0.6343341 0.0928609 -6.831010 0.0320928 0.0249505 0e+00 0.0000011 1.0000000
chr9 78298725 0.8388640 0.3907398 0.4481243 0.0605865 7.396440 0.0309085 0.0247160 0e+00 0.0000000 1.0000000
chr4 68631389 0.8561769 0.4396369 0.4165400 0.0552734 7.535994 0.0306055 0.0247160 0e+00 0.0000000 1.0000000
chr16 25736213 0.8879520 0.4478406 0.4401115 0.0594097 7.408079 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr4 53444246 0.8356875 0.3285169 0.5071705 0.0711664 7.126542 0.0295565 0.0233895 0e+00 0.0000002 1.0000000
chr11 58510051 0.4963456 0.1938293 0.3025162 0.0354587 8.531500 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr12 22798661 0.6544533 0.9815682 -0.3271148 0.0397775 -8.223622 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr16 6678849 0.6663221 0.2630799 0.4032422 0.0531885 7.581373 0.0295565 0.0252318 0e+00 0.0000000 1.0000000
chr4 5960726 0.9737809 0.6259282 0.3478527 0.0434981 7.996954 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr6 130407595 0.8234772 0.3971035 0.4263737 0.0575234 7.412178 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr6 79999871 0.9732801 0.5497729 0.4235072 0.0572802 7.393602 0.0297784 0.0247160 0e+00 0.0000000 1.0000000
chr15 4704441 0.3189473 0.7816072 -0.4626599 0.0642591 -7.199911 0.0305288 0.0247160 0e+00 0.0000001 1.0000000
chr14 113884863 0.9287166 0.5612661 0.3674505 0.0475206 7.732443 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr13 117802683 0.9491244 0.6835764 0.2655480 0.0294682 9.011350 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr1 164531928 0.9267018 0.6310210 0.2956809 0.0348750 8.478316 0.0297118 0.0247160 0e+00 0.0000000 1.0000000
chr16 79146302 0.5120750 0.9566142 -0.4445392 0.0616207 -7.214116 0.0295565 0.0247160 0e+00 0.0000001 1.0000000
chr13 21401041 0.9815791 0.6859249 0.2956542 0.0350145 8.443772 0.0295918 0.0247160 0e+00 0.0000000 1.0000000
chr1 112945546 0.5561058 0.9198629 -0.3637571 0.0472092 -7.705219 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr5 61028879 0.5072967 0.9022107 -0.3949140 0.0528180 -7.476880 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr6 85847045 0.2947397 0.7713686 -0.4766288 0.0675219 -7.058875 0.0470047 0.0247160 0e+00 0.0000003 1.0000000
chr6 26579167 0.8742654 0.4834222 0.3908432 0.0522738 7.476840 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 63737881 0.9731810 0.4143711 0.5588099 0.0824860 6.774605 0.0298782 0.0224680 0e+00 0.0000015 1.0000000
chr7 61306787 0.7884031 0.2444842 0.5439189 0.0803404 6.770180 0.0281041 0.0245288 0e+00 0.0000015 1.0000000
chr16 97660239 0.9615740 0.4582326 0.5033414 0.0731509 6.880866 0.0295565 0.0247160 0e+00 0.0000008 1.0000000
chr4 29806144 0.9724133 0.6353236 0.3370898 0.0430190 7.835831 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr7 142035173 0.5695608 0.2846996 0.2848612 0.0335505 8.490525 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr15 24617601 0.6462258 0.9304542 -0.2842284 0.0336137 -8.455739 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr1 92587661 0.9518741 0.4845321 0.4673420 0.0671702 6.957583 0.0270895 0.0190973 0e+00 0.0000005 1.0000000
chr7 39359902 0.7271109 0.4158437 0.3112672 0.0386341 8.056808 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chrX 106315938 0.5366811 0.9806512 -0.4439701 0.0630438 -7.042251 0.0295565 0.0247160 0e+00 0.0000003 1.0000000
chr14 44357435 0.6352171 0.9582174 -0.3230003 0.0408890 -7.899439 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr13 54690771 0.8742488 0.5550095 0.3192393 0.0402151 7.938286 0.0304374 0.0247160 0e+00 0.0000000 1.0000000
chr7 23564057 0.7801789 0.3643686 0.4158103 0.0579861 7.170858 0.0295565 0.0247160 0e+00 0.0000001 1.0000000
chrY 23311495 0.9712430 0.4263273 0.5449157 0.0817082 6.669047 0.0296781 0.0233895 0e+00 0.0000027 1.0000000
chr12 113239576 0.9410495 0.6665548 0.2744946 0.0321714 8.532260 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr3 64563620 0.2752680 0.6868999 -0.4116320 0.0575182 -7.156554 0.0295565 0.0247160 0e+00 0.0000001 1.0000000
chrX 138083239 0.9696800 0.4540550 0.5156250 0.0767598 6.717388 0.0296187 0.0247160 0e+00 0.0000021 1.0000000
chr13 111480638 0.8691008 0.6000099 0.2690909 0.0312838 8.601617 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr5 5592372 0.5678363 0.9575193 -0.3896829 0.0537482 -7.250153 0.0295565 0.0247160 0e+00 0.0000001 1.0000000
chr15 74818156 0.6502287 0.9740195 -0.3237908 0.0415658 -7.789838 0.0295565 0.0247943 0e+00 0.0000000 1.0000000
chr16 3414552 0.7026186 0.9732059 -0.2705873 0.0316857 -8.539737 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr1 110257365 0.7233406 0.9695952 -0.2462546 0.0272148 -9.048563 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr1 101781474 0.9630570 0.4133050 0.5497519 0.0838587 6.555694 0.0296360 0.0247160 0e+00 0.0000052 1.0000000
chr9 26456610 0.7495570 0.4091978 0.3403592 0.0448386 7.590767 0.0295565 0.0247160 0e+00 0.0000000 1.0000000
chr3 125805929 0.9154165 0.3984021 0.5170144 0.0778503 6.641138 0.0301164 0.0239720 0e+00 0.0000033 1.0000000
chrX 80918891 0.3746941 0.8042488 -0.4295546 0.0615708 -6.976600 0.0295565 0.0247160 0e+00 0.0000005 1.0000000
chr2 68870366 0.7483467 0.3098253 0.4385214 0.0633059 6.927021 0.0295565 0.0247160 0e+00 0.0000006 1.0000000
chrX 109993892 0.3431116 0.8837548 -0.5406432 0.0824448 -6.557637 0.0331619 0.0249059 0e+00 0.0000052 1.0000000
chr12 65443031 0.8123113 0.3797869 0.4325244 0.0622720 6.945733 0.0295565 0.0247160 0e+00 0.0000005 1.0000000
chrY 8807115 0.9632802 0.2582820 0.7049982 0.1135257 6.210032 0.0296360 0.0268709 0e+00 0.0000343 1.0000000
chr3 56460543 0.4166529 0.7720436 -0.3553907 0.0479578 -7.410495 0.0295565 0.0233895 0e+00 0.0000000 0.9999999
chr2 118554218 0.6880137 0.2527595 0.4352542 0.0629825 6.910720 0.0306920 0.0278885 0e+00 0.0000007 0.9999999
chr6 106329905 0.9790086 0.7178889 0.2611197 0.0302882 8.621165 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr9 26858501 0.4831569 0.8491618 -0.3660049 0.0500111 -7.318471 0.0295565 0.0247160 0e+00 0.0000001 0.9999999
chr1 33575722 0.4209817 0.6588251 -0.2378434 0.0259803 -9.154762 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr16 70506597 0.8698221 0.4264358 0.4433863 0.0648448 6.837654 0.0285818 0.0222404 0e+00 0.0000010 0.9999999
chr1 145018486 0.2811593 0.8592834 -0.5781240 0.0904411 -6.392271 0.0281862 0.0202248 0e+00 0.0000129 0.9999999
chr2 166670506 0.7074447 0.2043858 0.5030589 0.0763157 6.591812 0.0295565 0.0247160 0e+00 0.0000043 0.9999999
chr11 55794420 0.5608292 0.9331158 -0.3722866 0.0516104 -7.213409 0.0295565 0.0247160 0e+00 0.0000001 0.9999999
chr6 10234509 0.6979895 0.9703771 -0.2723876 0.0327138 -8.326390 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr1 157954959 0.5751130 0.9461839 -0.3710709 0.0514910 -7.206518 0.0295565 0.0247160 0e+00 0.0000001 0.9999999
chr13 66750758 0.3933393 0.7112252 -0.3178860 0.0415533 -7.650072 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chrX 91829326 0.9684355 0.5096887 0.4587468 0.0684543 6.701506 0.0295565 0.0247160 0e+00 0.0000023 0.9999999
chr7 107762209 0.9728341 0.5028102 0.4700239 0.0707765 6.640957 0.0296126 0.0247160 0e+00 0.0000033 0.9999999
chr4 12363869 0.8954715 0.4685082 0.4269633 0.0625795 6.822739 0.0295565 0.0247160 0e+00 0.0000011 0.9999999
chr14 5044282 0.3568783 0.8559586 -0.4990803 0.0763933 -6.533037 0.0295565 0.0249505 0e+00 0.0000058 0.9999999
chr4 135643375 0.6623323 0.9536344 -0.2913022 0.0366297 -7.952626 0.0295565 0.0248566 0e+00 0.0000000 0.9999999
chr7 18333018 0.6937270 0.9641493 -0.2704223 0.0326461 -8.283458 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr5 106135711 0.8520911 0.4256814 0.4264097 0.0625677 6.815175 0.0295565 0.0247160 0e+00 0.0000012 0.9999999
chr1 50262723 0.8009139 0.4376613 0.3632525 0.0504710 7.197257 0.0295565 0.0247160 0e+00 0.0000001 0.9999999
chr2 62969164 0.5289352 0.7916409 -0.2627057 0.0312658 -8.402324 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr15 25263320 0.5027092 0.9665574 -0.4638482 0.0701146 -6.615568 0.0317938 0.0247160 0e+00 0.0000038 0.9999999
chr14 24332371 0.4832286 0.9092819 -0.4260534 0.0628518 -6.778700 0.0295565 0.0248637 0e+00 0.0000015 0.9999999
chr6 112075711 0.6574740 0.9719082 -0.3144343 0.0413521 -7.603832 0.0295565 0.0247579 0e+00 0.0000000 0.9999999
chr4 139652953 0.3641915 0.8823918 -0.5182003 0.0806797 -6.422936 0.0261208 0.0212268 0e+00 0.0000110 0.9999999
chr12 114369747 0.2943185 0.7809684 -0.4866499 0.0746851 -6.516028 0.0295565 0.0247160 0e+00 0.0000064 0.9999999
chrX 82341432 0.2633671 0.8867775 -0.6234104 0.1011589 -6.162687 0.0262893 0.0247160 0e+00 0.0000440 0.9999999
chr7 106595271 0.9680671 0.6777143 0.2903527 0.0368174 7.886288 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr10 55949441 0.9827840 0.6376879 0.3450960 0.0474307 7.275798 0.0295565 0.0230616 0e+00 0.0000001 0.9999999
chrX 150123321 0.5979127 0.9161718 -0.3182591 0.0422465 -7.533385 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr9 91079699 0.9663788 0.3480061 0.6183727 0.1003397 6.162792 0.0298424 0.0227107 0e+00 0.0000440 0.9999999
chr6 129967580 0.7520569 0.4744224 0.2776345 0.0344679 8.054867 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr6 69479684 0.3110766 0.8947265 -0.5836498 0.0939931 -6.209494 0.0268534 0.0244617 0e+00 0.0000343 0.9999999
chr13 13181652 0.7744670 0.4471784 0.3272887 0.0441812 7.407871 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr17 8602766 0.7314628 0.4222917 0.3091711 0.0407076 7.594927 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr3 74479819 0.9712754 0.6568339 0.3144415 0.0417678 7.528318 0.0295565 0.0247160 0e+00 0.0000000 0.9999999
chr13 109027747 0.6322715 0.9777126 -0.3454411 0.0478205 -7.223711 0.0324493 0.0248102 0e+00 0.0000001 0.9999999
chr7 72586564 0.9772111 0.5545586 0.4226525 0.0628853 6.721004 0.0298767 0.0231763 0e+00 0.0000020 0.9999999
chrX 159099240 0.9360928 0.3972505 0.5388423 0.0855793 6.296409 0.0317555 0.0247160 0e+00 0.0000217 0.9999999
chr7 119555551 0.9777782 0.6039864 0.3737918 0.0535237 6.983675 0.0296486 0.0240364 0e+00 0.0000004 0.9999998
chr14 102006925 0.9170523 0.5334077 0.3836447 0.0554927 6.913423 0.0299302 0.0247160 0e+00 0.0000007 0.9999998
chr2 151384652 0.3015755 0.6284269 -0.3268514 0.0443883 -7.363461 0.0295565 0.0247160 0e+00 0.0000000 0.9999998
chr1 32960497 0.9811196 0.7637577 0.2173618 0.0229828 9.457591 0.0295565 0.0247160 0e+00 0.0000000 0.9999998
chr2 147959465 0.6775236 0.9670179 -0.2894943 0.0371787 -7.786562 0.0295565 0.0247160 0e+00 0.0000000 0.9999998
chr6 148615307 0.2148480 0.7270403 -0.5121923 0.0810531 -6.319215 0.0298001 0.0237825 0e+00 0.0000192 0.9999998
chrX 90463409 0.9587710 0.4599663 0.4988047 0.0785366 6.351240 0.0295565 0.0260160 0e+00 0.0000160 0.9999998
chrX 139454250 0.9590266 0.3971630 0.5618635 0.0912026 6.160607 0.0295565 0.0267968 0e+00 0.0000443 0.9999998
chr13 120152241 0.6124615 0.9441629 -0.3317013 0.0457804 -7.245495 0.0295565 0.0252847 0e+00 0.0000001 0.9999998
chr5 10732904 0.8193385 0.2148265 0.6045120 0.0999231 6.049773 0.0295565 0.0263710 0e+00 0.0000781 0.9999998
chr16 83556400 0.8389321 0.4785090 0.3604231 0.0516554 6.977446 0.0264540 0.0247160 0e+00 0.0000004 0.9999998
chr1 102133393 0.7244833 0.2982838 0.4261995 0.0647609 6.581128 0.0295565 0.0247160 0e+00 0.0000046 0.9999998
chr1 13032749 0.9257324 0.6116494 0.3140830 0.0425131 7.387917 0.0295565 0.0247160 0e+00 0.0000000 0.9999998
chr3 109437307 0.5990775 0.9749204 -0.3758430 0.0548568 -6.851351 0.0331193 0.0247160 0e+00 0.0000010 0.9999998
chr18 76788286 0.3022042 0.9541593 -0.6519550 0.1098060 -5.937334 0.0295565 0.0247160 0e+00 0.0001376 0.9999998
chr13 65209851 0.8351794 0.3477259 0.4874535 0.0771107 6.321475 0.0304083