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 0.0297484 0e+00 0.0000190 0.9999997
chr14 4380564 0.9142438 0.6586805 0.2555633 0.0309669 8.252783 0.0295565 0.0247160 0e+00 0.0000000 0.9999997
chr10 35694362 0.5900115 0.9577620 -0.3677505 0.0533252 -6.896367 0.0295565 0.0247160 0e+00 0.0000007 0.9999997
chr13 21813555 0.2127119 0.6258671 -0.4131552 0.0623775 -6.623464 0.0295565 0.0247160 0e+00 0.0000036 0.9999997
chr13 21813557 0.2127119 0.6258671 -0.4131552 0.0623775 -6.623464 0.0295565 0.0247160 0e+00 0.0000036 0.9999997
chr17 44031591 0.5432054 0.9601868 -0.4169814 0.0631757 -6.600348 0.0295565 0.0247160 0e+00 0.0000041 0.9999997
chr1 98013482 0.6540764 0.3110191 0.3430573 0.0485027 7.072957 0.0295565 0.0247160 0e+00 0.0000002 0.9999997
chr1 81618208 0.5131880 0.8731594 -0.3599714 0.0519656 -6.927108 0.0295565 0.0247160 0e+00 0.0000006 0.9999997
chrX 114310355 0.9831623 0.4757946 0.5073677 0.0815137 6.224324 0.0299527 0.0235096 0e+00 0.0000319 0.9999997
chr4 111965355 0.9526452 0.4508575 0.5017876 0.0804020 6.240987 0.0295565 0.0247160 0e+00 0.0000291 0.9999997
chr2 134813552 0.9045478 0.4635236 0.4410242 0.0682672 6.460261 0.0244046 0.0237334 0e+00 0.0000088 0.9999997
chr12 119889105 0.9284061 0.4647372 0.4636689 0.0728958 6.360705 0.0295565 0.0247160 0e+00 0.0000153 0.9999997
chr9 82394132 0.6968745 0.9777572 -0.2808826 0.0362585 -7.746677 0.0295565 0.0247484 0e+00 0.0000000 0.9999997
chr14 19554608 0.9711126 0.5454875 0.4256251 0.0652962 6.518376 0.0296170 0.0247160 0e+00 0.0000063 0.9999997
chrX 169913640 0.9533490 0.5518540 0.4014950 0.0604944 6.636894 0.0295565 0.0247160 0e+00 0.0000033 0.9999997
chr1 62051565 0.6150208 0.8796471 -0.2646263 0.0330354 -8.010395 0.0295565 0.0247160 0e+00 0.0000000 0.9999997
chr7 4460236 0.4868713 0.9046224 -0.4177511 0.0638274 -6.545011 0.0295565 0.0247160 0e+00 0.0000055 0.9999997
chr5 3227432 0.5414643 0.8792564 -0.3377921 0.0477757 -7.070382 0.0295565 0.0247160 0e+00 0.0000003 0.9999997
chr8 33949925 0.4548241 0.8841884 -0.4293643 0.0662373 -6.482213 0.0249542 0.0247160 0e+00 0.0000077 0.9999997
chr14 44096007 0.7008153 0.9775802 -0.2767649 0.0355669 -7.781525 0.0295565 0.0247160 0e+00 0.0000000 0.9999997
chr12 41967152 0.9739844 0.6684617 0.3055227 0.0413996 7.379839 0.0295565 0.0247160 0e+00 0.0000000 0.9999997
chr1 83496050 0.7484728 0.4521252 0.2963476 0.0395522 7.492575 0.0295565 0.0247160 0e+00 0.0000000 0.9999997
chr14 84301180 0.7567692 0.9761414 -0.2193722 0.0240984 -9.103194 0.0295565 0.0247160 0e+00 0.0000000 0.9999996
chr5 139466092 0.9602366 0.7088747 0.2513619 0.0305576 8.225836 0.0295565 0.0247160 0e+00 0.0000000 0.9999996
chr12 67839816 0.6222379 0.9291791 -0.3069412 0.0418386 -7.336320 0.0295565 0.0247160 0e+00 0.0000000 0.9999996
chr14 81376342 0.9504273 0.6974239 0.2530034 0.0309378 8.177803 0.0295565 0.0247160 0e+00 0.0000000 0.9999996
chr1 178036341 0.9017919 0.4149338 0.4868581 0.0783117 6.216929 0.0255605 0.0285485 0e+00 0.0000331 0.9999996
chr2 118553561 0.8157073 0.4875109 0.3281964 0.0462015 7.103592 0.0300060 0.0247160 0e+00 0.0000002 0.9999996
chr13 17224595 0.9234418 0.6110971 0.3123447 0.0430269 7.259294 0.0295565 0.0247160 0e+00 0.0000001 0.9999996
chr15 42275304 0.7705562 0.3975971 0.3729590 0.0553244 6.741315 0.0295565 0.0247160 0e+00 0.0000018 0.9999996
chr5 69582786 0.9632802 0.5601732 0.4031070 0.0614354 6.561479 0.0296360 0.0247160 0e+00 0.0000051 0.9999996
chr2 41460767 0.5225368 0.8759521 -0.3534153 0.0514774 -6.865442 0.0316802 0.0247160 0e+00 0.0000009 0.9999996
chr13 21813548 0.2127119 0.6258671 -0.4131552 0.0636411 -6.491959 0.0295565 0.0233895 0e+00 0.0000074 0.9999996
chr13 21813550 0.2127119 0.6258671 -0.4131552 0.0636430 -6.491760 0.0295565 0.0255866 0e+00 0.0000074 0.9999996
chrY 43784236 0.5463431 0.9466177 -0.4002745 0.0610261 -6.559075 0.0295565 0.0247160 0e+00 0.0000051 0.9999996
chr8 72197176 0.6993533 0.9730688 -0.2737154 0.0353151 -7.750671 0.0295565 0.0247160 0e+00 0.0000000 0.9999996
chr11 55460039 0.2503898 0.7833714 -0.5329816 0.0880720 -6.051661 0.0238776 0.0229102 0e+00 0.0000776 0.9999996
chrX 24568909 0.4269829 0.9669200 -0.5399371 0.0895636 -6.028532 0.0263621 0.0247160 0e+00 0.0000870 0.9999995
chr7 4460258 0.4921864 0.9035949 -0.4114084 0.0634437 -6.484627 0.0295565 0.0247160 0e+00 0.0000076 0.9999995
chr7 4460259 0.4921864 0.9035949 -0.4114084 0.0634437 -6.484627 0.0295565 0.0247160 0e+00 0.0000076 0.9999995
chr12 63491021 0.9383328 0.6797008 0.2586320 0.0323214 8.001884 0.0296828 0.0247160 0e+00 0.0000000 0.9999995
chr9 88516862 0.9757448 0.6356105 0.3401343 0.0490484 6.934671 0.0295565 0.0247160 0e+00 0.0000006 0.9999995
chr11 27183867 0.3889456 0.8266856 -0.4377401 0.0690059 -6.343512 0.2965952 0.0219313 0e+00 0.0000167 0.9999995
chr16 69683910 0.9755942 0.6902839 0.2853103 0.0378802 7.531915 0.0295565 0.0247160 0e+00 0.0000000 0.9999995
chr15 17129211 0.6058852 0.8905800 -0.2846948 0.0379124 -7.509270 0.0295565 0.0247160 0e+00 0.0000000 0.9999994
chr17 74483679 0.7960006 0.3664979 0.4295027 0.0676705 6.346969 0.0295565 0.0247160 0e+00 0.0000164 0.9999994
chr5 108295440 0.5186524 0.9702707 -0.4516183 0.0722238 -6.253037 0.0295565 0.0247160 0e+00 0.0000273 0.9999994
chr1 99024424 0.9735004 0.5846090 0.3888914 0.0595183 6.533984 0.0296126 0.0247160 0e+00 0.0000058 0.9999994
chr10 76592221 0.8090069 0.5089417 0.3000652 0.0412625 7.272097 0.0295565 0.0247160 0e+00 0.0000001 0.9999994
chr17 34143658 0.9346141 0.6114138 0.3232003 0.0460419 7.019705 0.0295565 0.0247160 0e+00 0.0000003 0.9999994
chr3 50204552 0.9098992 0.4973522 0.4125469 0.0645192 6.394168 0.0297682 0.0247160 0e+00 0.0000128 0.9999994
chr9 76304447 0.6327351 0.9611131 -0.3283780 0.0471723 -6.961245 0.0295565 0.0247160 0e+00 0.0000005 0.9999994
chr10 26161739 0.6970660 0.9789545 -0.2818885 0.0375977 -7.497494 0.0295565 0.0247774 0e+00 0.0000000 0.9999993
chr8 28137747 0.4252144 0.7594549 -0.3342405 0.0484405 -6.900016 0.0295565 0.0247160 0e+00 0.0000007 0.9999993
chr5 11510163 0.9039505 0.4897871 0.4141633 0.0649773 6.373968 0.0295565 0.0247160 0e+00 0.0000143 0.9999993
chr9 6388544 0.7031934 0.9832506 -0.2800572 0.0372587 -7.516564 0.0295565 0.0249236 0e+00 0.0000000 0.9999993
chr7 8373643 0.1330384 0.5838749 -0.4508364 0.0725989 -6.209964 0.0302172 0.0242877 0e+00 0.0000343 0.9999993
chr8 56043866 0.5072430 0.8290164 -0.3217733 0.0459127 -7.008376 0.0295565 0.0247160 0e+00 0.0000004 0.9999993
chr1 25983709 0.9723556 0.6183226 0.3540330 0.0526317 6.726607 0.0295565 0.0273055 0e+00 0.0000020 0.9999993
chr6 8192429 0.7592507 0.9789431 -0.2196924 0.0248182 -8.852061 0.0295565 0.0247160 0e+00 0.0000000 0.9999993
chr10 108849915 0.6653244 0.9647891 -0.2994647 0.0413761 -7.237619 0.0295565 0.0247160 0e+00 0.0000001 0.9999993
chrY 81240504 0.2161061 0.9036771 -0.6875710 0.1219538 -5.637961 0.0295565 0.0247160 0e+00 0.0005635 0.9999993
chr6 129616102 0.8709866 0.4674021 0.4035845 0.0631313 6.392777 0.0295565 0.0247160 0e+00 0.0000129 0.9999992
chrX 127625239 0.9167500 0.4496591 0.4670909 0.0763538 6.117451 0.0263208 0.0233895 0e+00 0.0000555 0.9999992
chr1 145018485 0.2811593 0.8592834 -0.5781240 0.0996432 -5.801944 0.0327969 0.0263851 0e+00 0.0002655 0.9999992
chr19 26074127 0.9004010 0.5594102 0.3409908 0.0502948 6.779839 0.0295565 0.0247160 0e+00 0.0000014 0.9999992
chr10 97711357 0.8204094 0.4859337 0.3344757 0.0489608 6.831493 0.0295565 0.0247160 0e+00 0.0000011 0.9999992
chrX 119624531 0.9749660 0.5731014 0.4018646 0.0631151 6.367166 0.0297630 0.0233895 0e+00 0.0000148 0.9999991
chrX 127687508 0.9039970 0.4154511 0.4885460 0.0813002 6.009157 0.0300003 0.0247160 0e+00 0.0000958 0.9999991
chr6 79882205 0.6283305 0.9201517 -0.2918212 0.0401564 -7.267121 0.0295565 0.0248446 0e+00 0.0000001 0.9999991
chr10 64731476 0.9849606 0.6593949 0.3255657 0.0472638 6.888270 0.0298211 0.0233895 0e+00 0.0000008 0.9999991
chr2 158979636 0.2398473 0.6646927 -0.4248454 0.0680859 -6.239848 0.0368187 0.0247160 0e+00 0.0000292 0.9999991
chr3 102781963 0.9737809 0.6478280 0.3259529 0.0473707 6.880902 0.0295565 0.0247160 0e+00 0.0000008 0.9999991
chr9 6871163 0.9707468 0.5667232 0.4040236 0.0639167 6.321100 0.0295565 0.0266965 0e+00 0.0000190 0.9999990
chr1 92587660 0.9518741 0.4845321 0.4673420 0.0772930 6.046365 0.0344933 0.0194000 0e+00 0.0000795 0.9999990
chr13 20899672 0.6193555 0.3227198 0.2966356 0.0413972 7.165588 0.0295565 0.0247160 0e+00 0.0000001 0.9999990
chr8 18107332 0.3772168 0.6778587 -0.3006420 0.0422567 -7.114662 0.0295565 0.0247160 0e+00 0.0000002 0.9999990
chr3 6866092 0.4005777 0.8118627 -0.4112850 0.0656168 -6.267984 0.0295565 0.0247160 0e+00 0.0000252 0.9999990
chr4 4908560 0.9295296 0.5081287 0.4214009 0.0677514 6.219813 0.0307506 0.0247160 0e+00 0.0000327 0.9999990
chr4 91533703 0.9809634 0.7447236 0.2362398 0.0287270 8.223611 0.0295935 0.0247160 0e+00 0.0000000 0.9999989
chr1 148952469 0.5948528 0.9673083 -0.3724555 0.0574607 -6.481912 0.0295565 0.0248593 0e+00 0.0000077 0.9999989
chr2 131432298 0.9202392 0.5923608 0.3278784 0.0480633 6.821802 0.0295565 0.0233895 0e+00 0.0000011 0.9999989
chr7 61306786 0.7884031 0.2444842 0.5439189 0.0936359 5.808874 0.0330839 0.0221244 0e+00 0.0002576 0.9999989
chr4 58258116 0.9799661 0.6449084 0.3350577 0.0495960 6.755740 0.0296647 0.0247160 0e+00 0.0000016 0.9999989
chr7 4460294 0.5089517 0.9017130 -0.3927612 0.0617937 -6.356012 0.0295565 0.0247160 0e+00 0.0000156 0.9999989
chr13 21813542 0.2127119 0.6258671 -0.4131552 0.0661171 -6.248836 0.0295565 0.0274928 0e+00 0.0000278 0.9999989
chr2 176741639 0.5769809 0.9612985 -0.3843176 0.0600295 -6.402151 0.0295565 0.0247160 0e+00 0.0000122 0.9999989
chrY 29073344 0.4674906 0.8408070 -0.3733164 0.0577531 -6.464009 0.0295565 0.0258403 0e+00 0.0000086 0.9999989
chr2 40085571 0.9845358 0.5693351 0.4152007 0.0666204 6.232331 0.0299461 0.0238986 0e+00 0.0000305 0.9999989
chr11 47156428 0.9680768 0.5669226 0.4011542 0.0636937 6.298172 0.0295565 0.0247160 0e+00 0.0000216 0.9999989
chr8 116812489 0.9756943 0.5552081 0.4204862 0.0677826 6.203450 0.0296054 0.0253707 0e+00 0.0000355 0.9999989
chr11 74031780 0.6587398 0.9150615 -0.2563218 0.0331069 -7.742247 0.0295565 0.0247160 0e+00 0.0000000 0.9999988
chr10 24562761 0.7640756 0.2604397 0.5036359 0.0855576 5.886514 0.0295565 0.0247160 0e+00 0.0001760 0.9999988
chrX 152859803 0.4717225 0.9675561 -0.4958336 0.0839368 -5.907229 0.0261208 0.0250479 0e+00 0.0001593 0.9999988
chr9 41635120 0.5649030 0.8905137 -0.3256107 0.0478597 -6.803438 0.0295565 0.0247160 0e+00 0.0000013 0.9999988
chr7 128812783 0.9743621 0.6610395 0.3133226 0.0452543 6.923593 0.0295565 0.0247160 0e+00 0.0000006 0.9999988
chr16 52284354 0.5043113 0.8968805 -0.3925693 0.0620975 -6.321819 0.0295565 0.0247160 0e+00 0.0000190 0.9999988
chr14 83027559 0.5985073 0.9257104 -0.3272031 0.0482592 -6.780114 0.0295565 0.0247160 0e+00 0.0000014 0.9999987
chr9 13014345 0.8757682 0.5952290 0.2805392 0.0383500 7.315238 0.0295565 0.0247160 0e+00 0.0000001 0.9999987
chr1 8750172 0.9448513 0.6778979 0.2669534 0.0354643 7.527393 0.0296772 0.0247160 0e+00 0.0000000 0.9999987
chr10 38595133 0.9681910 0.6186565 0.3495345 0.0530485 6.588967 0.0295565 0.0247160 0e+00 0.0000044 0.9999987
chr4 95837598 0.9764442 0.6030049 0.3734393 0.0582246 6.413775 0.0297496 0.0271522 0e+00 0.0000115 0.9999987
chr12 22455255 0.8868415 0.3919276 0.4949139 0.0841667 5.880163 0.0295565 0.0247160 0e+00 0.0001815 0.9999986
GL456221.1 23700 0.8475829 0.3893486 0.4582343 0.0763568 6.001223 0.0295565 0.0247160 0e+00 0.0000995 0.9999986
chr1 67487876 0.8448760 0.5640132 0.2808628 0.0385650 7.282846 0.0295565 0.0247160 0e+00 0.0000001 0.9999986
chr8 4806027 0.9134656 0.5634507 0.3500149 0.0533300 6.563184 0.0295565 0.0247160 0e+00 0.0000050 0.9999986
chr8 4806104 0.9134656 0.5634507 0.3500149 0.0533300 6.563184 0.0295565 0.0247160 0e+00 0.0000050 0.9999986
chr8 81808473 0.8978481 0.5872014 0.3106468 0.0449484 6.911192 0.0276810 0.0247160 0e+00 0.0000007 0.9999986
chr4 96512233 0.6231628 0.9118045 -0.2886417 0.0403407 -7.155100 0.0295565 0.0247160 0e+00 0.0000001 0.9999985
chr18 58546537 0.8071804 0.4663441 0.3408363 0.0515589 6.610624 0.0295565 0.0247160 0e+00 0.0000039 0.9999985
chr13 21813539 0.2121426 0.6189352 -0.4067927 0.0658065 -6.181649 0.0295565 0.0275829 0e+00 0.0000399 0.9999984
chr13 25905875 0.4716347 0.9703808 -0.4987461 0.0855343 -5.830948 0.0278671 0.0247612 0e+00 0.0002306 0.9999984
chr18 50961156 0.6117392 0.9701556 -0.3584164 0.0554472 -6.464108 0.0295565 0.0247612 0e+00 0.0000086 0.9999984
chr7 14457598 0.7809117 0.4807591 0.3001526 0.0429583 6.987068 0.0295565 0.0247160 0e+00 0.0000004 0.9999984
chr18 44292096 0.7395781 0.9776316 -0.2380536 0.0296337 -8.033191 0.0295565 0.0247160 0e+00 0.0000000 0.9999984
chr15 87094366 0.9738652 0.7421644 0.2317007 0.0282736 8.194961 0.0295565 0.0247160 0e+00 0.0000000 0.9999984
chrX 73319150 0.2838955 0.7999482 -0.5160527 0.0893462 -5.775878 0.0303558 0.0225647 0e+00 0.0002994 0.9999984
chr4 108696464 0.9000935 0.5841520 0.3159415 0.0464207 6.806050 0.0295565 0.0247160 0e+00 0.0000012 0.9999984
chr8 104677130 0.5756256 0.9572983 -0.3816727 0.0605571 -6.302692 0.0295565 0.0247160 0e+00 0.0000211 0.9999984
chr6 113073844 0.7569123 0.4981345 0.2587778 0.0341639 7.574593 0.0295565 0.0247160 0e+00 0.0000000 0.9999983
chr12 115178409 0.9719831 0.6352909 0.3366922 0.0509301 6.610867 0.0295565 0.0247160 0e+00 0.0000039 0.9999983
chr18 70108477 0.8850669 0.5371169 0.3479500 0.0533591 6.520912 0.0295565 0.0247160 0e+00 0.0000062 0.9999983
chr1 74875804 0.9391851 0.6052648 0.3339203 0.0503940 6.626191 0.0295565 0.0247160 0e+00 0.0000036 0.9999983
chr13 65767110 0.6449867 0.9737010 -0.3287143 0.0493652 -6.658823 0.0295565 0.0247550 0e+00 0.0000029 0.9999982
chrY 13440325 0.3225767 0.7591082 -0.4365316 0.0726429 -6.009276 0.0295565 0.0247160 0e+00 0.0000958 0.9999982
chr8 47728209 0.8725824 0.4943760 0.3782064 0.0600597 6.297174 0.0260942 0.0234097 0e+00 0.0000217 0.9999982
chr5 31629796 0.2535130 0.6432090 -0.3896960 0.0625441 -6.230740 0.0295565 0.0247160 0e+00 0.0000308 0.9999982
chr7 72586598 0.9772111 0.5545586 0.4226525 0.0696720 6.066322 0.0298767 0.0249141 0e+00 0.0000722 0.9999982
chrX 109224971 0.4842785 0.9616773 -0.4773988 0.0815025 -5.857471 0.0263175 0.0248353 0e+00 0.0002033 0.9999982
chr15 9254627 0.8939775 0.4641990 0.4297785 0.0712707 6.030224 0.0377118 0.0206435 0e+00 0.0000865 0.9999981
chr13 102515872 0.9807454 0.5019762 0.4787692 0.0819526 5.842025 0.0298958 0.0247160 0e+00 0.0002180 0.9999981
chr8 52131624 0.7560587 0.4442040 0.3118547 0.0458399 6.803132 0.0295565 0.0247160 0e+00 0.0000013 0.9999981
chr7 64057804 0.2809034 0.7334648 -0.4525614 0.0762996 -5.931374 0.0295565 0.0247160 0e+00 0.0001422 0.9999981
chr15 14829692 0.6512086 0.9729133 -0.3217047 0.0479949 -6.702896 0.0306960 0.0247160 0e+00 0.0000023 0.9999981
chr1 157955107 0.5751130 0.9461839 -0.3710709 0.0587058 -6.320852 0.0345081 0.0247160 0e+00 0.0000190 0.9999981
chr16 96874192 0.6213228 0.9770683 -0.3557455 0.0554227 -6.418771 0.0295565 0.0248507 0e+00 0.0000112 0.9999980
chrX 53995056 0.9755900 0.3272878 0.6483022 0.1188812 5.453364 0.0305283 0.0245323 0e+00 0.0013032 0.9999980
chr18 20129923 0.9814056 0.5021634 0.4792422 0.0822314 5.827975 0.0299385 0.0223491 0e+00 0.0002342 0.9999980
chr11 74534082 0.6529782 0.9793238 -0.3263456 0.0491006 -6.646466 0.0399453 0.0249520 0e+00 0.0000032 0.9999980
chr6 142263744 0.9464738 0.7206624 0.2258114 0.0273077 8.269143 0.0295565 0.0247160 0e+00 0.0000000 0.9999980
chr18 6745843 0.8854061 0.4706175 0.4147886 0.0684487 6.059845 0.0295565 0.0247160 0e+00 0.0000744 0.9999979
chr17 20130725 0.8791178 0.4125738 0.4665440 0.0798115 5.845571 0.0337995 0.0229956 0e+00 0.0002141 0.9999978
chrX 8673765 0.2851761 0.7692797 -0.4841037 0.0836435 -5.787703 0.0295565 0.0251748 0e+00 0.0002854 0.9999978
chr6 79050098 0.9281187 0.5399771 0.3881416 0.0628066 6.179949 0.0300348 0.0232074 0e+00 0.0000402 0.9999978
chrX 82341433 0.2633671 0.8867775 -0.6234104 0.1142335 -5.457333 0.0381515 0.0218750 0e+00 0.0012827 0.9999977
chr6 123126316 0.9811370 0.6528455 0.3282915 0.0499132 6.577250 0.0296306 0.0255072 0e+00 0.0000047 0.9999976
chr15 85161971 0.9153959 0.5410730 0.3743229 0.0600216 6.236466 0.0295565 0.0247160 0e+00 0.0000298 0.9999976
chr15 65747314 0.9682404 0.4611418 0.5070986 0.0891203 5.690044 0.0295565 0.0233895 0e+00 0.0004481 0.9999975
chr4 114351501 0.9146945 0.6471089 0.2675857 0.0367034 7.290491 0.0295565 0.0247160 0e+00 0.0000001 0.9999975
chr14 4999756 0.7814519 0.1546644 0.6267876 0.1154520 5.428989 0.0301281 0.0252677 1e-07 0.0014521 0.9999975
chrX 19581915 0.9501478 0.6429726 0.3071753 0.0454243 6.762359 0.0299651 0.0247160 0e+00 0.0000016 0.9999975
chr9 3051892 0.9797183 0.6358114 0.3439069 0.0535107 6.426887 0.0295975 0.0233895 0e+00 0.0000108 0.9999974
chr14 106210386 0.8074220 0.4270185 0.3804034 0.0615625 6.179142 0.0316917 0.0247160 0e+00 0.0000403 0.9999974
chrY 67927016 0.3514772 0.8517200 -0.5002428 0.0878830 -5.692148 0.0295565 0.0247160 0e+00 0.0004453 0.9999974
chr5 49353221 0.9779146 0.6165342 0.3613805 0.0573952 6.296351 0.0297378 0.0247160 0e+00 0.0000217 0.9999974
chr14 74419800 0.4909961 0.9062833 -0.4152872 0.0692644 -5.995684 0.0268184 0.0214329 0e+00 0.0001020 0.9999973
chr6 42095025 0.1907854 0.5976831 -0.4068977 0.0674803 -6.029876 0.0295565 0.0247160 0e+00 0.0000866 0.9999973
chr4 144329753 0.3273671 0.7600968 -0.4327298 0.0733365 -5.900606 0.0304748 0.0247160 0e+00 0.0001642 0.9999971
chrX 167503975 0.4684793 0.9757158 -0.5072365 0.0898262 -5.646862 0.0295565 0.0248966 0e+00 0.0005410 0.9999971
chr3 157819653 0.9774801 0.5374890 0.4399911 0.0750224 5.864796 0.0299843 0.0284705 0e+00 0.0001958 0.9999971
chrX 116004855 0.5058326 0.9018873 -0.3960547 0.0653888 -6.056923 0.0316711 0.0248755 0e+00 0.0000755 0.9999970
chr4 66294136 0.9619739 0.5493602 0.4126137 0.0690657 5.974218 0.0295565 0.0233895 0e+00 0.0001136 0.9999970
chr11 104825444 0.9214649 0.5142786 0.4071864 0.0679159 5.995454 0.0295565 0.0247160 0e+00 0.0001021 0.9999970
chrX 79891419 0.9248085 0.2957081 0.6291004 0.1171154 5.371628 0.0278944 0.0221243 1e-07 0.0018565 0.9999969
chr15 13159004 0.5993779 0.1725347 0.4268432 0.0723754 5.897632 0.0295565 0.0247160 0e+00 0.0001668 0.9999968
chr14 84097547 0.8402205 0.3479102 0.4923103 0.0868729 5.667018 0.0264280 0.0255877 0e+00 0.0004939 0.9999968
chr15 4696365 0.5276158 0.8724337 -0.3448179 0.0542275 -6.358729 0.0319764 0.0253221 0e+00 0.0000154 0.9999968
chr2 110450103 0.5086210 0.8820224 -0.3734014 0.0605628 -6.165523 0.0295565 0.0247160 0e+00 0.0000434 0.9999968
chr4 30461050 0.5074980 0.9636925 -0.4561945 0.0789749 -5.776448 0.0294943 0.0247160 0e+00 0.0002992 0.9999968
chr16 71583033 0.9861565 0.5982700 0.3878865 0.0638298 6.076888 0.0300740 0.0247160 0e+00 0.0000684 0.9999968
chr16 58662781 0.6712149 0.9181707 -0.2469558 0.0326405 -7.565938 0.0295565 0.0247160 0e+00 0.0000000 0.9999966
chr2 97302491 0.9248994 0.6268968 0.2980026 0.0439797 6.775919 0.0295565 0.0247160 0e+00 0.0000015 0.9999966
chrY 31748179 0.9186628 0.3685601 0.5501026 0.0999818 5.502027 0.0313939 0.0249955 0e+00 0.0010576 0.9999966
chr13 21813531 0.2149561 0.6152441 -0.4002880 0.0668049 -5.991896 0.0295565 0.0276322 0e+00 0.0001037 0.9999965
chr13 4205907 0.9680433 0.5963148 0.3717285 0.0604605 6.148284 0.0295565 0.0270369 0e+00 0.0000473 0.9999965
chr11 37475853 0.9277836 0.6786408 0.2491428 0.0331893 7.506715 0.0295565 0.0247160 0e+00 0.0000000 0.9999965
chr2 116089872 0.7035914 0.9385701 -0.2349786 0.0300546 -7.818403 0.0295565 0.0250799 0e+00 0.0000000 0.9999965
chr11 22798718 0.9012496 0.6581698 0.2430799 0.0318717 7.626822 0.0295565 0.0247160 0e+00 0.0000000 0.9999964
chr13 4412543 0.9091621 0.4027162 0.5064458 0.0906225 5.588520 0.0247126 0.0233895 0e+00 0.0007131 0.9999964
chr11 13151170 0.5505092 0.8929615 -0.3424523 0.0540640 -6.334199 0.0295565 0.0247160 0e+00 0.0000177 0.9999963
chr1 11577027 0.4419365 0.8298464 -0.3879099 0.0642263 -6.039734 0.0385979 0.0247160 0e+00 0.0000820 0.9999963
chr17 26343206 0.9629307 0.5353542 0.4275765 0.0730760 5.851125 0.0295565 0.0247160 0e+00 0.0002083 0.9999963
chr14 50176575 0.7205768 0.9696157 -0.2490390 0.0332593 -7.487805 0.0295565 0.0247612 0e+00 0.0000000 0.9999963
chr1 184315444 0.4146907 0.8419083 -0.4272176 0.0730648 -5.847102 0.0295565 0.0249910 0e+00 0.0002125 0.9999962
chrY 8065050 0.5210452 0.9810486 -0.4600034 0.0804250 -5.719658 0.0610924 0.0250730 0e+00 0.0003940 0.9999962
chr5 69417787 0.6768231 0.9143274 -0.2375044 0.0307186 -7.731624 0.0295565 0.0247160 0e+00 0.0000000 0.9999962
chr14 76650425 0.6476890 0.9736274 -0.3259384 0.0505108 -6.452843 0.0295565 0.0247160 0e+00 0.0000093 0.9999961
chr7 113358056 0.9769788 0.5563540 0.4206248 0.0716811 5.868002 0.0295565 0.0247160 0e+00 0.0001926 0.9999961
chr1 49777512 0.8443009 0.5073833 0.3369176 0.0529670 6.360902 0.0299279 0.0280210 0e+00 0.0000153 0.9999961
chr10 38377948 0.9184778 0.4615553 0.4569225 0.0798017 5.725725 0.0297320 0.0247160 0e+00 0.0003854 0.9999961
chr10 124818212 0.9882151 0.5623423 0.4258728 0.0729022 5.841700 0.0299422 0.0247858 0e+00 0.0002182 0.9999961
chr3 113009231 0.2254617 0.6864398 -0.4609781 0.0807980 -5.705315 0.0301570 0.0259255 0e+00 0.0004211 0.9999960
chr2 86013198 0.4600702 0.8842472 -0.4241770 0.0725683 -5.845214 0.0295565 0.0247160 0e+00 0.0002143 0.9999960
chr17 91877885 0.7708673 0.3837481 0.3871192 0.0642781 6.022568 0.0281869 0.0247160 0e+00 0.0000894 0.9999960
chrX 24289598 0.2680415 0.7376382 -0.4695968 0.0827821 -5.672687 0.0295565 0.0247160 0e+00 0.0004835 0.9999960
chr5 10477110 0.9651353 0.6629047 0.3022306 0.0453133 6.669800 0.0295565 0.0247160 0e+00 0.0000027 0.9999960
chr1 178036342 0.9017919 0.4149338 0.4868581 0.0866898 5.616094 0.0266707 0.0265273 0e+00 0.0006230 0.9999960
chrX 75168862 0.1450012 0.6828968 -0.5378957 0.0981294 -5.481496 0.0289059 0.0253788 0e+00 0.0011584 0.9999959
chr12 114769951 0.7329491 0.3992250 0.3337241 0.0523793 6.371300 0.0276810 0.0247160 0e+00 0.0000145 0.9999959
chr1 192255705 0.9432761 0.5246098 0.4186662 0.0714339 5.860891 0.0298122 0.0295410 0e+00 0.0001998 0.9999959
chr4 51117690 0.8489601 0.4860961 0.3628640 0.0589528 6.155164 0.0295565 0.0247160 0e+00 0.0000457 0.9999959
chr4 67422088 0.5538081 0.9731921 -0.4193841 0.0716465 -5.853518 0.0295565 0.0247160 0e+00 0.0002064 0.9999959
chr4 89869897 0.7552271 0.4582342 0.2969930 0.0442042 6.718662 0.0295565 0.0247160 0e+00 0.0000021 0.9999958
chr10 104485598 0.9842886 0.6435764 0.3407122 0.0540214 6.306985 0.0295857 0.0247160 0e+00 0.0000205 0.9999958
chr11 60452112 0.6936403 0.3666525 0.3269879 0.0510134 6.409841 0.0295565 0.0247160 0e+00 0.0000117 0.9999957
chrY 31748178 0.9186628 0.3685601 0.5501026 0.1011615 5.437865 0.0264488 0.0214917 1e-07 0.0013974 0.9999957
chr11 82696838 0.9798219 0.6951826 0.2846393 0.0415060 6.857782 0.0295975 0.0250116 0e+00 0.0000009 0.9999957
chrX 4064509 0.7418752 0.4132875 0.3285877 0.0514626 6.384981 0.0295565 0.0247160 0e+00 0.0000134 0.9999955
chr1 41170458 0.9465532 0.7122443 0.2343089 0.0302433 7.747471 0.0298013 0.0247160 0e+00 0.0000000 0.9999955
chr10 127799552 0.9324336 0.5743209 0.3581127 0.0581243 6.161157 0.0295565 0.0247160 0e+00 0.0000442 0.9999955
chrX 101623684 0.6625197 0.9737904 -0.3112706 0.0475964 -6.539793 0.0295565 0.0247160 0e+00 0.0000056 0.9999955
chr2 38485968 0.8187974 0.4956256 0.3231718 0.0502868 6.426577 0.0295565 0.0247160 0e+00 0.0000108 0.9999955
chr6 103761094 0.5371568 0.8724449 -0.3352881 0.0530190 -6.323930 0.0295565 0.0247160 0e+00 0.0000188 0.9999955
chr8 87557678 0.5326233 0.9315266 -0.3989033 0.0674304 -5.915780 0.0295565 0.0248238 0e+00 0.0001526 0.9999953
chrX 77874580 0.5582866 0.9692486 -0.4109620 0.0701831 -5.855567 0.0295565 0.0247160 0e+00 0.0002045 0.9999953
chr7 21121657 0.0909601 0.4732471 -0.3822870 0.0637260 -5.998919 0.0302081 0.0247160 0e+00 0.0001008 0.9999953
chr18 26619315 0.1436465 0.5831146 -0.4394681 0.0767204 -5.728179 0.0335225 0.0242877 0e+00 0.0003820 0.9999952
chr6 45718261 0.5396522 0.9353845 -0.3957323 0.0668513 -5.919589 0.0295565 0.0250011 0e+00 0.0001494 0.9999951
chrX 136456768 0.5060965 0.9702751 -0.4641786 0.0823476 -5.636823 0.0375663 0.0248478 0e+00 0.0005661 0.9999951
chr8 17610259 0.8062787 0.3583137 0.4479650 0.0787143 5.691027 0.0318071 0.0203755 0e+00 0.0004471 0.9999951
chr9 3312548 0.7024247 0.9218777 -0.2194530 0.0270313 -8.118465 0.0295565 0.0247160 0e+00 0.0000000 0.9999950
chrX 103467460 0.8746587 0.5121196 0.3625391 0.0595188 6.091169 0.0295565 0.0247160 0e+00 0.0000631 0.9999949
chr13 78867970 0.6403067 0.9721814 -0.3318747 0.0525904 -6.310561 0.0295565 0.0248000 0e+00 0.0000201 0.9999948
chr4 20400093 0.8518110 0.5075252 0.3442857 0.0554106 6.213355 0.0295565 0.0247160 0e+00 0.0000337 0.9999948
chr3 75865836 0.8731742 0.5068966 0.3662775 0.0604042 6.063779 0.0286486 0.0247160 0e+00 0.0000730 0.9999948
chr2 97491449 0.9220821 0.6100392 0.3120428 0.0481113 6.485853 0.0295565 0.0247160 0e+00 0.0000076 0.9999948
chr7 139956281 0.8652998 0.5223813 0.3429185 0.0551461 6.218363 0.0295565 0.0247160 0e+00 0.0000329 0.9999947
chr6 70292049 0.6957541 0.9784017 -0.2826476 0.0414660 -6.816372 0.0295565 0.0247160 0e+00 0.0000012 0.9999947
chr18 3999770 0.9727126 0.5563540 0.4163586 0.0718226 5.797045 0.0295565 0.0247160 0e+00 0.0002720 0.9999947
chr6 47308856 0.5936641 0.8725378 -0.2788737 0.0406121 -6.866766 0.0295565 0.0247160 0e+00 0.0000009 0.9999947
chr17 34274472 0.9374804 0.5419154 0.3955650 0.0671352 5.892061 0.0321911 0.0215437 0e+00 0.0001710 0.9999947
chr7 23446406 0.2916986 0.6637576 -0.3720590 0.0618035 -6.020028 0.0295565 0.0247160 0e+00 0.0000907 0.9999946
chr11 51267780 0.8403500 0.4405417 0.3998083 0.0681302 5.868295 0.0325979 0.0245730 0e+00 0.0001925 0.9999946
chr6 110089182 0.4986132 0.9692666 -0.4706534 0.0842663 -5.585309 0.0294943 0.0247160 0e+00 0.0007236 0.9999946
chr9 59579092 0.6704937 0.2937489 0.3767448 0.0629340 5.986349 0.0295565 0.0247160 0e+00 0.0001068 0.9999945
chr4 114270577 0.2957850 0.8958804 -0.6000954 0.1137813 -5.274115 0.0280249 0.0268035 1e-07 0.0028223 0.9999945
chr3 71382659 0.4021595 0.7054744 -0.3033149 0.0463217 -6.548007 0.0295565 0.0247160 0e+00 0.0000054 0.9999943
chrX 50919222 0.9809717 0.5610542 0.4199175 0.0729103 5.759374 0.0299367 0.0247160 0e+00 0.0003264 0.9999943
chr12 18385646 0.4677186 0.8961674 -0.4284488 0.0749006 -5.720229 0.0549106 0.0247160 0e+00 0.0003934 0.9999942
chr4 67781790 0.9284761 0.5472114 0.3812647 0.0641675 5.941714 0.0262950 0.0247160 0e+00 0.0001347 0.9999942
chr4 10985153 0.9491164 0.6486373 0.3004792 0.0457425 6.568928 0.0303506 0.0233895 0e+00 0.0000049 0.9999941
chr1 80986808 0.4716704 0.9755747 -0.5039043 0.0921602 -5.467702 0.0259815 0.0248594 0e+00 0.0012267 0.9999941
chr7 42279513 0.2262495 0.6709241 -0.4446746 0.0786808 -5.651631 0.0313760 0.0254529 0e+00 0.0005296 0.9999941
chr13 9351462 0.3104698 0.8018543 -0.4913845 0.0893846 -5.497417 0.0268454 0.0242974 0e+00 0.0010789 0.9999940
chr2 67974945 0.9034476 0.5815931 0.3218545 0.0506717 6.351754 0.0295565 0.0247160 0e+00 0.0000160 0.9999940
chr17 12821825 0.9721733 0.6573313 0.3148420 0.0490857 6.414127 0.0295565 0.0247160 0e+00 0.0000115 0.9999940
chr5 4195309 0.5930069 0.2889271 0.3040798 0.0466284 6.521343 0.0271971 0.0247160 0e+00 0.0000062 0.9999940
chr11 90427659 0.5514235 0.9631822 -0.4117587 0.0712351 -5.780276 0.0295565 0.0247160 0e+00 0.0002947 0.9999940
chr7 39155741 0.6771746 0.3284484 0.3487262 0.0568392 6.135307 0.0363960 0.0247160 0e+00 0.0000509 0.9999940
chr18 4184336 0.2394624 0.6005780 -0.3611156 0.0596838 -6.050476 0.0295565 0.0247160 0e+00 0.0000779 0.9999939
chr17 94171458 0.4550573 0.8701642 -0.4151070 0.0720281 -5.763126 0.0276810 0.0247160 0e+00 0.0003195 0.9999939
chr15 13645559 0.5881246 0.9572812 -0.3691566 0.0615469 -5.997973 0.0295565 0.0247160 0e+00 0.0001011 0.9999939
chrY 9180560 0.9719899 0.6202964 0.3516935 0.0575628 6.109738 0.0295565 0.0247160 0e+00 0.0000574 0.9999939
chrX 14295780 0.7930669 0.4065806 0.3864863 0.0655657 5.894643 0.0295565 0.0247160 0e+00 0.0001689 0.9999938
chr5 12385374 0.6153095 0.9649406 -0.3496311 0.0571510 -6.117675 0.0295565 0.0247160 0e+00 0.0000555 0.9999937
chr8 17764673 0.8470829 0.3806819 0.4664010 0.0838887 5.559759 0.0336914 0.0253215 0e+00 0.0008160 0.9999937
chr1 134946562 0.8201379 0.4697958 0.3503421 0.0573591 6.107873 0.0295565 0.0247160 0e+00 0.0000578 0.9999936
chr7 42683158 0.9721733 0.6308781 0.3412952 0.0552870 6.173157 0.0295565 0.0247160 0e+00 0.0000416 0.9999936
chr6 131688351 0.7354584 0.3826685 0.3527898 0.0579392 6.088969 0.0303225 0.0247160 0e+00 0.0000638 0.9999936
chr14 97422172 0.8479505 0.4333425 0.4146080 0.0721190 5.748946 0.0274421 0.0233895 0e+00 0.0003459 0.9999936
chrY 69264474 0.9032030 0.4396018 0.4636013 0.0833734 5.560542 0.0295565 0.0247160 0e+00 0.0008132 0.9999935
chr15 15967871 0.5700592 0.2882906 0.2817686 0.0416921 6.758320 0.0295565 0.0247160 0e+00 0.0000016 0.9999935
chr4 94783023 0.5908002 0.1304085 0.4603916 0.0826967 5.567232 0.0295565 0.0247160 0e+00 0.0007885 0.9999934
chr8 73866839 0.9809920 0.6326378 0.3483542 0.0569924 6.112288 0.0295565 0.0247160 0e+00 0.0000569 0.9999934
chrX 114284428 0.7962566 0.3183759 0.4778807 0.0867311 5.509910 0.0261208 0.0267492 0e+00 0.0010234 0.9999934
chr12 79143276 0.9864623 0.6635333 0.3229290 0.0511763 6.310135 0.0297844 0.0228557 0e+00 0.0000202 0.9999934
chr7 4460448 0.5082839 0.8454130 -0.3371291 0.0544374 -6.192964 0.0295565 0.0249794 0e+00 0.0000376 0.9999934
chr13 98515165 0.8946194 0.5666260 0.3279934 0.0523492 6.265490 0.0295565 0.0247160 0e+00 0.0000256 0.9999934
chr7 17092233 0.6563770 0.9799930 -0.3236160 0.0513539 -6.301678 0.0300195 0.0249100 0e+00 0.0000212 0.9999933
chrX 138703494 0.9809566 0.5835873 0.3973693 0.0683075 5.817364 0.0297097 0.0233895 0e+00 0.0002461 0.9999933
chr12 114488910 0.2867097 0.6926239 -0.4059142 0.0703322 -5.771386 0.0275925 0.0250670 0e+00 0.0003054 0.9999932
chrY 2486721 0.8898423 0.3243802 0.5654620 0.1070255 5.283432 0.0276810 0.0254214 1e-07 0.0027105 0.9999932
chr11 10825923 0.3643751 0.7906446 -0.4262694 0.0750268 -5.681559 0.0286748 0.0233895 0e+00 0.0004641 0.9999932
chrX 63737880 0.9731810 0.4143711 0.5588099 0.1055114 5.296204 0.0298364 0.0230615 1e-07 0.0025653 0.9999931
chr17 92541873 0.7420949 0.9691370 -0.2270420 0.0292437 -7.763801 0.0295565 0.0247160 0e+00 0.0000000 0.9999930
chrX 78317341 0.2236633 0.8579974 -0.6343341 0.1230317 -5.155859 0.0263213 0.0245534 3e-07 0.0045185 0.9999930
chr14 72987526 0.5810512 0.9755078 -0.3944566 0.0678119 -5.816923 0.0257864 0.0249604 0e+00 0.0002465 0.9999929
chr14 4999755 0.7814519 0.1546644 0.6267876 0.1213286 5.166035 0.0281478 0.0252677 2e-07 0.0043581 0.9999929
chr8 113262094 0.6773621 0.2375550 0.4398072 0.0782696 5.619133 0.0281757 0.0281246 0e+00 0.0006145 0.9999929
chr17 39682078 0.4480528 0.9150968 -0.4670441 0.0846310 -5.518591 0.0247505 0.0233895 0e+00 0.0009844 0.9999928
chrY 5034413 0.8480344 0.3546177 0.4934167 0.0907248 5.438609 0.0295565 0.0247160 1e-07 0.0013960 0.9999928
chrX 119772501 0.9688319 0.5128560 0.4559760 0.0821003 5.553890 0.0300182 0.0247160 0e+00 0.0008386 0.9999927
chr10 16102342 0.4815882 0.8995081 -0.4179199 0.0733233 -5.699685 0.0261262 0.0231295 0e+00 0.0004317 0.9999927
chr18 6275295 0.4581242 0.8715281 -0.4134039 0.0723180 -5.716477 0.0295565 0.0247160 0e+00 0.0003993 0.9999927
chr7 9161289 0.2383240 0.6898080 -0.4514841 0.0811181 -5.565764 0.0295565 0.0247160 0e+00 0.0007927 0.9999926
chr11 28799806 0.2873274 0.7667372 -0.4794099 0.0876161 -5.471708 0.0372985 0.0212471 0e+00 0.0012080 0.9999926
chr8 55554224 0.7473343 0.4332918 0.3140425 0.0494289 6.353417 0.0295565 0.0247160 0e+00 0.0000158 0.9999926
chr3 155706989 0.9350707 0.6453355 0.2897352 0.0438257 6.611072 0.0295565 0.0247160 0e+00 0.0000039 0.9999925
chr12 92824420 0.4589197 0.1217639 0.3371559 0.0548353 6.148521 0.0295565 0.0247160 0e+00 0.0000473 0.9999924
chr16 41958986 0.9275966 0.5629494 0.3646472 0.0611960 5.958679 0.0243601 0.0225655 0e+00 0.0001235 0.9999924
chr13 106887020 0.8505891 0.4412855 0.4093036 0.0715239 5.722611 0.0276810 0.0247160 0e+00 0.0003887 0.9999924
chrX 127614338 0.2707385 0.8612628 -0.5905243 0.1134733 -5.204080 0.0273359 0.0249505 2e-07 0.0037259 0.9999923
chr9 7704414 0.9682728 0.5071512 0.4611216 0.0835663 5.518030 0.0296222 0.0247160 0e+00 0.0009862 0.9999922
chr17 38188242 0.3513643 0.8616653 -0.5103010 0.0949623 -5.373724 0.0307104 0.0247160 1e-07 0.0018419 0.9999922
chr3 120473648 0.4428711 0.8819620 -0.4390909 0.0785463 -5.590220 0.0295565 0.0249031 0e+00 0.0007083 0.9999921
chrX 149855419 0.4256452 0.9649446 -0.5392994 0.1017821 -5.298570 0.0349612 0.0248729 1e-07 0.0025418 0.9999921
chr3 71066872 0.8738126 0.5363212 0.3374914 0.0550764 6.127691 0.0295565 0.0247160 0e+00 0.0000527 0.9999919
chr7 4460302 0.5089517 0.9017130 -0.3927612 0.0679008 -5.784336 0.0295565 0.0247160 0e+00 0.0002900 0.9999919
chr2 108843965 0.8321973 0.3893221 0.4428752 0.0795664 5.566107 0.0250121 0.0254983 0e+00 0.0007918 0.9999918
chrX 168920286 0.2047624 0.6263750 -0.4216126 0.0746511 -5.647773 0.0300992 0.0247160 0e+00 0.0005390 0.9999918
chr7 4460526 0.5048037 0.8436160 -0.3388123 0.0554411 -6.111212 0.0295565 0.0247160 0e+00 0.0000570 0.9999917
chr16 19691826 0.7705255 0.4043882 0.3661373 0.0618203 5.922603 0.0301534 0.0257345 0e+00 0.0001474 0.9999917
chr18 79180964 0.8915470 0.5439334 0.3476136 0.0575266 6.042658 0.0295565 0.0247160 0e+00 0.0000809 0.9999916
chrY 8065051 0.5210452 0.9810486 -0.4600034 0.0836387 -5.499887 0.0246432 0.0250316 0e+00 0.0010669 0.9999916
chr7 84893439 0.9436888 0.6055771 0.3381117 0.0553229 6.111609 0.0295565 0.0247160 0e+00 0.0000570 0.9999916
chr6 60157927 0.7184147 0.9793334 -0.2609187 0.0373946 -6.977439 0.0303642 0.0247160 0e+00 0.0000004 0.9999916
chr1 102981617 0.7342455 0.2352698 0.4989758 0.0927282 5.381059 0.0265436 0.0247160 1e-07 0.0017778 0.9999916
chr6 11143391 0.6660171 0.9429035 -0.2768863 0.0411232 -6.733098 0.0295565 0.0247160 0e+00 0.0000019 0.9999915
chrX 32593518 0.9762773 0.6896665 0.2866108 0.0433856 6.606129 0.0296996 0.0253603 0e+00 0.0000040 0.9999915
chr6 68200172 0.6468372 0.9803739 -0.3335367 0.0543266 -6.139471 0.0276810 0.0247446 0e+00 0.0000498 0.9999914
chr5 46355308 0.9737809 0.7270989 0.2466820 0.0341278 7.228173 0.0295565 0.0247160 0e+00 0.0000001 0.9999914
chrY 9180544 0.9719899 0.6202964 0.3516935 0.0585836 6.003272 0.0295565 0.0247160 0e+00 0.0000984 0.9999913
chr5 68232770 0.6279858 0.9326139 -0.3046281 0.0476388 -6.394542 0.0295565 0.0247160 0e+00 0.0000128 0.9999913
chr9 93115883 0.8873648 0.5354144 0.3519504 0.0586730 5.998504 0.0295565 0.0247160 0e+00 0.0001009 0.9999912
chr2 95419474 0.9752830 0.6869431 0.2883399 0.0438616 6.573862 0.0295565 0.0247160 0e+00 0.0000048 0.9999912


DMRs
Number of differentially methylated regions = 57
chr start end length nCG meanMethy1 meanMethy2 diff.Methy areaStat
chr2 118553430 118555268 1839 94 0.7870175 0.4957842 0.2912332 453.1723532
chr11 12026385 12026598 214 77 0.6119100 0.3443702 0.2675398 359.3215172
chr2 170131224 170131437 214 78 0.4888923 0.2118775 0.2770148 355.2445636
chr7 4460236 4460602 367 46 0.5118860 0.8628514 -0.3509654 -243.9431943
chr13 21813165 21813557 393 48 0.2766057 0.6043927 -0.3277870 -230.9210984
chr11 57401191 57401414 224 46 0.7303141 0.9619184 -0.2316043 -199.7287207
chr18 10051950 10052246 297 45 0.7043129 0.4467014 0.2576115 196.8847385
chr11 106033014 106033282 269 38 0.6375780 0.3166770 0.3209009 149.6361430
chr19 38030876 38031008 133 32 0.6530744 0.3042199 0.3488544 148.8517368
chrY 90829118 90829322 205 31 0.3986220 0.7021705 -0.3035485 -143.9014588
chr19 6497423 6497544 122 33 0.6265544 0.2631697 0.3633847 124.9050657
chr13 100593771 100593930 160 24 0.8510290 0.4590183 0.3920107 117.1438893
chr11 82930999 82931084 86 26 0.2385177 0.5178142 -0.2792965 -108.8063498
chr3 32397402 32397462 61 25 0.4242702 0.2069284 0.2173418 108.4620714
chr6 112729128 112729226 99 23 0.5444765 0.2413386 0.3031379 82.0303685
chr6 47763255 47763390 136 22 0.7549811 0.3678090 0.3871721 75.6585781
chr4 134160675 134160775 101 14 0.6631614 0.3675291 0.2956323 60.3496156
chr17 81572051 81572106 56 14 0.8801270 0.5295789 0.3505481 59.6767643
chr2 174284534 174284611 78 8 0.3300649 0.5785344 -0.2484695 -33.9334913
chr1 157954959 157955208 250 6 0.5751130 0.9461839 -0.3710709 -29.6743360
chr1 134400199 134400252 54 8 0.7226482 0.4210778 0.3015704 29.0798308
chr13 66306065 66306174 110 5 0.4616184 0.8979929 -0.4363745 -28.3146956
chr1 170894035 170894184 150 6 0.4654344 0.8331686 -0.3677343 -26.4447214
chr6 27051395 27051512 118 6 0.9381867 0.6020377 0.3361490 25.0065957
chr11 55804066 55804132 67 7 0.9119487 0.4908437 0.4211050 24.2791473
chr2 172307236 172307288 53 6 0.7788332 0.4391368 0.3396963 23.2447328
chrX 164287093 164287220 128 6 0.3753824 0.7795761 -0.4041938 -23.1318170
chr11 22401409 22401485 77 5 0.9529909 0.5465774 0.4064135 20.8587028
chr4 121500611 121500721 111 5 0.8283546 0.4365757 0.3917788 19.8709437
chrX 49154321 49154392 72 4 0.5384062 0.9485955 -0.4101893 -19.7357719
chr3 127688424 127688482 59 5 0.8319735 0.4966977 0.3352758 18.7008701
chr7 76609796 76609865 70 4 0.6017644 0.9416468 -0.3398823 -18.2518162
chr17 6499012 6499065 54 6 0.9299196 0.5715462 0.3583734 18.0154052
chrY 43223787 43223854 68 5 0.7024850 0.9646248 -0.2621398 -17.8480496
chrY 67927016 67927084 69 4 0.3514772 0.8517200 -0.5002428 -17.6654978
chr17 21003301 21003474 174 4 0.9462952 0.6601961 0.2860991 17.0020501
chr6 116485964 116486019 56 4 0.6723904 0.9668669 -0.2944765 -16.9265552
chr12 6126259 6126355 97 4 0.8630546 0.5193609 0.3436937 16.7480016
chrY 9413418 9413631 214 4 0.8922974 0.5499446 0.3423527 16.6235136
chr16 13734307 13734511 205 4 0.5415071 0.7995721 -0.2580650 -16.5673645
chr10 121302988 121303053 66 4 0.7328173 0.3760440 0.3567733 16.5384883
chrX 168920286 168920372 87 4 0.2047624 0.6263750 -0.4216126 -16.4777290
chr14 14257152 14257371 220 4 0.6171087 0.2928153 0.3242934 16.3934988
chr7 75273897 75274017 121 4 0.8081989 0.4635372 0.3446617 16.3172293
chr13 33257077 33257324 248 4 0.7934703 0.4310657 0.3624046 16.2114056
chr16 40333886 40334021 136 4 0.9009603 0.5655452 0.3354151 16.0143519
chr7 47251559 47251666 108 4 0.3020550 0.6506383 -0.3485833 -16.0065468
chrX 106206325 106206554 230 5 0.8544391 0.5416956 0.3127435 15.8513731
chrX 118663146 118663207 62 4 0.6720007 0.2732084 0.3987923 15.3019512
chr7 138617762 138617847 86 4 0.4763239 0.8198048 -0.3434809 -15.1882471
chrX 56214823 56214877 55 4 0.2464776 0.6281596 -0.3816820 -15.0207312
chrX 134399237 134399289 53 4 0.8709843 0.4988587 0.3721256 14.4185016
chr13 43460006 43460060 55 4 0.7035675 0.3187925 0.3847750 14.2923107
chrX 153893196 153893320 125 4 0.3852613 0.7510654 -0.3658041 -13.3010252
chrY 2529987 2530473 487 4 0.6168532 0.6165433 0.0003099 -2.6529874
chr5 102215775 102216108 334 4 0.7263788 0.6977556 0.0286232 0.2758992
chrX 149707106 149707944 839 4 0.5847924 0.5437296 0.0410628 -0.0518087
Visualization of individual DMR



R session information

R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US       
 [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US   
 [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C 

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] knitr_1.29                  ggplot2_3.3.2              
 [3] kableExtra_1.2.1            dplyr_1.0.0                
 [5] gdata_2.18.0                DSS_2.36.0                 
 [7] bsseq_1.24.4                SummarizedExperiment_1.18.2
 [9] DelayedArray_0.14.1         matrixStats_0.56.0         
[11] GenomicRanges_1.40.0        GenomeInfoDb_1.24.2        
[13] IRanges_2.22.2              S4Vectors_0.26.1           
[15] BiocParallel_1.22.0         Biobase_2.48.0             
[17] BiocGenerics_0.34.0         rmarkdown_2.3              

loaded via a namespace (and not attached):
 [1] httr_1.4.2                jsonlite_1.7.0           
 [3] viridisLite_0.3.0         splines_4.0.1            
 [5] DelayedMatrixStats_1.10.1 R.utils_2.9.2            
 [7] gtools_3.8.2              highr_0.8                
 [9] BSgenome_1.56.0           GenomeInfoDbData_1.2.3   
[11] Rsamtools_2.4.0           yaml_2.2.1               
[13] pillar_1.4.6              lattice_0.20-41          
[15] glue_1.4.1                limma_3.44.3             
[17] digest_0.6.25             XVector_0.28.0           
[19] rvest_0.3.6               colorspace_1.4-1         
[21] htmltools_0.5.0           Matrix_1.2-18            
[23] R.oo_1.23.0               XML_3.99-0.5             
[25] pkgconfig_2.0.3           zlibbioc_1.34.0          
[27] purrr_0.3.4               scales_1.1.1             
[29] webshot_0.5.2             HDF5Array_1.16.1         
[31] tibble_3.0.3              generics_0.0.2           
[33] ellipsis_0.3.1            withr_2.2.0              
[35] magrittr_1.5              crayon_1.3.4             
[37] evaluate_0.14             R.methodsS3_1.8.0        
[39] xml2_1.3.2                tools_4.0.1              
[41] data.table_1.13.0         lifecycle_0.2.0          
[43] stringr_1.4.0             Rhdf5lib_1.10.1          
[45] munsell_0.5.0             locfit_1.5-9.4           
[47] Biostrings_2.56.0         compiler_4.0.1           
[49] rlang_0.4.7               rhdf5_2.32.2             
[51] grid_4.0.1                RCurl_1.98-1.2           
[53] rstudioapi_0.11           bitops_1.0-6             
[55] base64enc_0.1-3           gtable_0.3.0             
[57] R6_2.4.1                  GenomicAlignments_1.24.0 
[59] rtracklayer_1.48.0        permute_0.9-5            
[61] stringi_1.4.6             Rcpp_1.0.5               
[63] vctrs_0.3.2               tidyselect_1.1.0         
[65] xfun_0.16                
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