library(DSS)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

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    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
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Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: BiocParallel
Loading required package: bsseq
Loading required package: GenomicRanges
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library(bsseq)
library(dplyr)

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library(kableExtra)

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library(ggplot2)
library(knitr)

Preprocessing

# read in sample names
samples <- read.table(file="../scripts/allsamples.txt", sep="\t", header=F, stringsAsFactors=F)$V1

# read in methylation data in tab delimited format: <chromosome> <position> <count total> <count methylated>
dat.list <- vector(mode = "list", length = length(samples))

for (i in 1:length(samples)){
        dat.list[[i]] <- read.table(paste0("../04-Methylation/", samples[i], ".CpG.counts.txt"), header=F, col.names=c("chr", "pos", "N", "X"))
}


# save BSseqData for future easy loading
BSobj <- makeBSseqData(dat.list, samples)
save(BSobj, file="BSobj.RData")
#load("BSobj.RData")


The original data included 1418084 CpG sites across all samples.

# remove the CpG sites on un-placed contigs
chr.use <- paste0("chr", c(1:22, "M", "X", "Y"))
dat <- chrSelectBSseq(BSobj, seqnames= chr.use, order=T)


CpG sites from unplaced contigs were removed, leaving 1418084 CpG sites.

Multidimensional scaling (MDS) plot of raw methylation data. 

# create meta data for samples
stage <- c(rep("3M", 3), rep("24M", 3))
pdata <- data.frame(Samples=samples, EM.stage=stage, stringsAsFactors=F)
pdata$EM.stage <- factor(pdata$EM.stage, levels=c("3M", "24M"))
idx <- match(samples, pdata$Samples)
pdata <- pdata[idx,]

# set plot point type for the two groups
pchs <- ifelse(pdata$EM.stage == "3M", 15, 16)
# MDS plot
pct.meth <- getMeth(dat, type = "raw")
limma::plotMDS(asin(pct.meth), col = "blue", pch = pchs)
legend("bottomright", title = "EM.stage", legend = levels(pdata$EM.stage), pch = unique(pchs), text.font = 0.8)


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


# differential methylation 24M vs 3M test (Wald test)
dmlTest <- DMLtest(BSobj, group1=samples[1:3], group2=samples[4:6], smoothing=TRUE)
Smoothing ...
Estimating dispersion for each CpG site, this will take a while ...

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Computing test statistics ...
# save test result for future easy loading
save(dmlTest, file="DML.RData")
# loading previously saved test results
#load("DML.RData")

#
# call differentially methylated CpG sites
dmls <- callDML(dmlTest, p.threshold=1.0)
# write DML results to file
write.table(dmls, file="Differential_methylation_CpG_24Mvs3M.txt", sep="\t", col.names=T, row.names=F, quote=F)


# list the top 500 differentially methylated CpG sites (ordered by P values)
n <- ncol(dmls)
header1 <- n
names(header1) <- paste0("Number of differentially methylated CpGs with FDR adjusted P < 0.05 = ", length(which(dmls$fdr < 0.05)))
header2 <- n
names(header2) <- "Top 500 CpG sites"
kable(dmls[1:500,], align = 'c', row.names=F) %>%
  add_header_above(header1, align = 'l') %>%
  add_header_above(header2, font_size = "larger", bold = T, align = "l") %>%
  kable_styling(bootstrap_options = c("hover", "condensed", "responsive"), full_width = T) %>%
  scroll_box(height = "500px")
Top 500 CpG sites
Number of differentially methylated CpGs with FDR adjusted P < 0.05 = 137
chr pos mu1 mu2 diff diff.se stat phi1 phi2 pval fdr postprob.overThreshold
chr18 27705890 0.1359743 0.5992355 -0.4632612 0.0570730 -8.116999 0.0454689 0.0295088 0.0000000 0.0000000 1.0000000
chr18 76788275 0.3031786 0.9576704 -0.6544918 0.0887605 -7.373682 0.0415192 0.0265846 0.0000000 0.0000000 1.0000000
chr18 76788286 0.3031786 0.9576704 -0.6544918 0.1106945 -5.912596 0.0415192 0.0265846 0.0000000 0.0002041 0.9999997
chr18 50961156 0.6125266 0.9724943 -0.3599677 0.0549520 -6.550586 0.0415192 0.0266366 0.0000000 0.0000080 0.9999989
chr18 44292096 0.7404710 0.9793312 -0.2388602 0.0293626 -8.134852 0.0415192 0.0265846 0.0000000 0.0000000 0.9999989
chr18 70108477 0.8861006 0.5387680 0.3473326 0.0532635 6.521027 0.0415192 0.0265846 0.0000000 0.0000088 0.9999983
chr18 6745843 0.8882682 0.4724788 0.4157894 0.0682040 6.096263 0.0415192 0.0265846 0.0000000 0.0000797 0.9999982
chr18 58546537 0.8069866 0.4685227 0.3384639 0.0516097 6.558142 0.0415192 0.0265846 0.0000000 0.0000080 0.9999981
chr18 20129923 0.9828184 0.5034878 0.4793306 0.0822035 5.831024 0.0419663 0.0237288 0.0000000 0.0003071 0.9999980
chr18 3999770 0.9749734 0.5588323 0.4161411 0.0715029 5.819915 0.0415192 0.0265846 0.0000000 0.0003156 0.9999951
chr18 6275295 0.4570788 0.8741066 -0.4170278 0.0719800 -5.793661 0.0415192 0.0265846 0.0000000 0.0003555 0.9999947
chr18 4184336 0.2399108 0.6033839 -0.3634731 0.0600421 -6.053640 0.0415192 0.0265846 0.0000000 0.0000987 0.9999943
chr18 26619315 0.1445599 0.5849468 -0.4403870 0.0776969 -5.668014 0.0464096 0.0260469 0.0000000 0.0005753 0.9999941
chr18 79180964 0.8933565 0.5461697 0.3471868 0.0575781 6.029844 0.0415192 0.0265846 0.0000000 0.0001089 0.9999912
chr18 4897829 0.7851835 0.3603503 0.4248332 0.0758113 5.603824 0.0415192 0.0265846 0.0000000 0.0007494 0.9999909
chr18 88339401 0.9882562 0.6061936 0.3820626 0.0680518 5.614290 0.0422176 0.0650805 0.0000000 0.0007240 0.9999830
chr18 3236960 0.6936342 0.9863807 -0.2927465 0.0471871 -6.203957 0.0384476 0.0269248 0.0000000 0.0000451 0.9999779
chr18 26499595 0.9004923 0.5984799 0.3020125 0.0495162 6.099263 0.0415192 0.0265846 0.0000000 0.0000797 0.9999775
chr18 88339402 0.9882562 0.6061936 0.3820626 0.0699310 5.463420 0.0425735 0.0460826 0.0000000 0.0012671 0.9999725
chr18 3941121 0.7638484 0.9781954 -0.2143469 0.0285076 -7.518946 0.0415192 0.0265846 0.0000000 0.0000000 0.9999698
chr18 41447117 0.9355798 0.6914643 0.2441155 0.0361056 6.761155 0.0415192 0.0265846 0.0000000 0.0000027 0.9999672
chr18 7987276 0.5680178 0.1379195 0.4300983 0.0831024 5.175521 0.0366147 0.0242206 0.0000002 0.0050283 0.9999644
chr18 32885208 0.4920893 0.8385519 -0.3464627 0.0622052 -5.569678 0.0415192 0.0265846 0.0000000 0.0008676 0.9999629
chr18 17178540 0.6580969 0.9669160 -0.3088191 0.0537681 -5.743539 0.0415192 0.0265846 0.0000000 0.0004456 0.9999486
chr18 52050734 0.8637562 0.5120838 0.3516725 0.0651998 5.393769 0.0415192 0.0265846 0.0000001 0.0018071 0.9999433
chr18 20129922 0.9828184 0.5034878 0.4793306 0.0988049 4.851286 0.0424017 0.0280688 0.0000012 0.0178097 0.9999383
chr18 15652492 0.9448666 0.7554247 0.1894418 0.0234593 8.075351 0.0415192 0.0265846 0.0000000 0.0000000 0.9999313
chr18 10429512 0.4397118 0.8296125 -0.3899007 0.0762119 -5.116005 0.0415192 0.0269402 0.0000003 0.0060452 0.9999288
chr18 71966059 0.9134439 0.5994790 0.3139649 0.0562960 5.577041 0.0415192 0.0249688 0.0000000 0.0008525 0.9999279
chr18 42284660 0.7565171 0.3721742 0.3843429 0.0751273 5.115887 0.0354818 0.0237543 0.0000003 0.0060452 0.9999231
chr18 85448173 0.9728425 0.5493923 0.4234502 0.0854933 4.953022 0.0419311 0.0252422 0.0000007 0.0123902 0.9999226
chr18 43406349 0.8018325 0.5624849 0.2393476 0.0376616 6.355216 0.0415192 0.0265846 0.0000000 0.0000186 0.9998922
chr18 14379317 0.5713505 0.8773970 -0.3060465 0.0558574 -5.479070 0.0415192 0.0265846 0.0000000 0.0011919 0.9998873
chr18 49811791 0.7033488 0.9152131 -0.2118644 0.0303522 -6.980205 0.0415192 0.0265846 0.0000000 0.0000007 0.9998859
chr18 37381665 0.7933874 0.3620615 0.4313259 0.0899469 4.795338 0.0347356 0.0228079 0.0000016 0.0221922 0.9998850
chr18 71483695 0.5810713 0.9535608 -0.3724896 0.0746322 -4.991004 0.0402160 0.0288120 0.0000006 0.0104654 0.9998694
chr18 48548491 0.9842397 0.6903757 0.2938640 0.0532758 5.515903 0.0416337 0.0268697 0.0000000 0.0010933 0.9998631
chr18 18480278 0.9764181 0.5821617 0.3942564 0.0811759 4.856819 0.0415801 0.0317455 0.0000012 0.0176879 0.9998555
chr18 60275148 0.9212132 0.5518046 0.3694085 0.0756316 4.884314 0.0415192 0.0289262 0.0000010 0.0162546 0.9998161
chr18 9829221 0.7945722 0.4509168 0.3436554 0.0688171 4.993751 0.0435908 0.0289113 0.0000006 0.0104481 0.9998004
chr18 89676668 0.9429154 0.6164613 0.3264540 0.0640528 5.096638 0.0415192 0.0265846 0.0000003 0.0065122 0.9997964
chr18 86660572 0.5066879 0.7734085 -0.2667206 0.0472849 -5.640712 0.0415192 0.0265846 0.0000000 0.0006380 0.9997890
chr18 33755271 0.6342991 0.9735533 -0.3392542 0.0682688 -4.969391 0.0415192 0.0265846 0.0000007 0.0115574 0.9997713
chr18 52895307 0.9800047 0.6523109 0.3276938 0.0652861 5.019353 0.0418297 0.0266478 0.0000005 0.0093850 0.9997563
chr18 73134688 0.3599157 0.7096348 -0.3497191 0.0717099 -4.876861 0.0415192 0.0265846 0.0000011 0.0165097 0.9997515
chr18 77994796 0.5450973 0.8373093 -0.2922120 0.0557638 -5.240170 0.0449213 0.0265846 0.0000002 0.0039230 0.9997165
chr18 66616018 0.8125584 0.4389725 0.3735859 0.0798641 4.677771 0.0488357 0.0248238 0.0000029 0.0342566 0.9996933
chr18 18480277 0.9764181 0.5821617 0.3942564 0.0859589 4.586568 0.0425286 0.0222314 0.0000045 0.0486359 0.9996906
chr18 10967246 0.4686354 0.8767019 -0.4080665 0.0905834 -4.504873 0.0440032 0.0273233 0.0000066 0.0629719 0.9996642
chr18 3205594 0.9709460 0.7101680 0.2607780 0.0473033 5.512892 0.0415192 0.0265846 0.0000000 0.0010933 0.9996617
chr18 90098340 0.6263634 0.9094402 -0.2830768 0.0538976 -5.252122 0.0415192 0.0265846 0.0000002 0.0038104 0.9996590
chr18 41592048 0.8129749 0.4631494 0.3498255 0.0737910 4.740758 0.0427871 0.0277121 0.0000021 0.0274792 0.9996449
chr18 51079163 0.2965761 0.6958993 -0.3993231 0.0885437 -4.509898 0.0413836 0.0224421 0.0000065 0.0626075 0.9996383
chr18 46315308 0.9820364 0.7008343 0.2812022 0.0536186 5.244491 0.0416167 0.0230912 0.0000002 0.0039006 0.9996369
chr18 87623436 0.5946804 0.9352656 -0.3405851 0.0719362 -4.734547 0.0393866 0.0266360 0.0000022 0.0280536 0.9995877
chr18 76788287 0.3031786 0.9576704 -0.6544918 0.1665195 -3.930420 0.0384168 0.0275475 0.0000848 0.3030617 0.9995685
chr18 89676609 0.9429154 0.6164613 0.3264540 0.0685775 4.760363 0.0416866 0.0265846 0.0000019 0.0254106 0.9995203
chr18 61467660 0.9421171 0.6711264 0.2709907 0.0521576 5.195609 0.0422029 0.0265846 0.0000002 0.0046625 0.9994779
chr18 37381666 0.7933874 0.3620615 0.4313259 0.1013182 4.257142 0.0306790 0.0208473 0.0000207 0.1329971 0.9994626
chr18 8814172 0.9397416 0.5893603 0.3503814 0.0768225 4.560924 0.0435901 0.0255877 0.0000051 0.0514398 0.9994414
chr18 33788097 0.9147396 0.4992388 0.4155007 0.0973381 4.268634 0.0417711 0.0265846 0.0000197 0.1281222 0.9994051
chr18 33788099 0.9147396 0.4992388 0.4155007 0.0973381 4.268634 0.0417711 0.0265846 0.0000197 0.1281222 0.9994051
chr18 88865298 0.7450399 0.9880315 -0.2429916 0.0441659 -5.501797 0.0360916 0.0269417 0.0000000 0.0011149 0.9993973
chr18 80205217 0.4990469 0.8488508 -0.3498039 0.0772385 -4.528883 0.0441498 0.0301098 0.0000059 0.0582038 0.9993901
chr18 24067280 0.7288889 0.5066694 0.2222195 0.0379929 5.848977 0.0415192 0.0265846 0.0000000 0.0002873 0.9993521
chr18 34092860 0.3636795 0.6892694 -0.3255899 0.0702411 -4.635322 0.0415192 0.0265846 0.0000036 0.0397391 0.9993401
chr18 71483694 0.5810713 0.9535608 -0.3724896 0.0848876 -4.388034 0.0423837 0.0202138 0.0000114 0.0916246 0.9993364
chr18 4426200 0.8328780 0.4708269 0.3620511 0.0821088 4.409409 0.0420621 0.0282472 0.0000104 0.0858812 0.9992924
chr18 7987275 0.5680178 0.1379195 0.4300983 0.1038430 4.141814 0.0343716 0.0298266 0.0000345 0.1752824 0.9992608
chr18 14184062 0.9536770 0.6486621 0.3050149 0.0645007 4.728861 0.0439552 0.0261835 0.0000023 0.0283518 0.9992598
chr18 54985324 0.6588352 0.9743579 -0.3155227 0.0678429 -4.650784 0.0415192 0.0265846 0.0000033 0.0380917 0.9992554
chr18 85498300 0.9333407 0.6403656 0.2929750 0.0607513 4.822531 0.0415192 0.0265846 0.0000014 0.0195618 0.9992546
chr18 29288186 0.9465243 0.6479676 0.2985567 0.0625564 4.772597 0.0426847 0.0230631 0.0000018 0.0241420 0.9992483
chr18 59986435 0.9191558 0.6964245 0.2227313 0.0389811 5.713823 0.0415192 0.0265846 0.0000000 0.0004812 0.9991794
chr18 3274893 0.6895518 0.9727220 -0.2831702 0.0583510 -4.852874 0.0415192 0.0265846 0.0000012 0.0178097 0.9991527
chr18 26915547 0.9261607 0.6427852 0.2833755 0.0585616 4.838928 0.0358505 0.0265846 0.0000013 0.0187581 0.9991299
chr18 39440899 0.8101954 0.4713326 0.3388628 0.0764860 4.430387 0.0356495 0.0290764 0.0000094 0.0823512 0.9991048
chr18 27705889 0.1359743 0.5992355 -0.4632612 0.1164741 -3.977377 0.0316748 0.0193844 0.0000697 0.2728157 0.9990928
chr18 72282562 0.8731957 0.5440641 0.3291316 0.0734796 4.479227 0.0722529 0.0249688 0.0000075 0.0691510 0.9990905
chr18 11137993 0.9396234 0.6449232 0.2947002 0.0624385 4.719850 0.0357553 0.0296920 0.0000024 0.0291125 0.9990904
chr18 6572038 0.6199008 0.9192658 -0.2993649 0.0641976 -4.663183 0.0334363 0.0256852 0.0000031 0.0364304 0.9990502
chr18 44946061 0.8991524 0.6719194 0.2272330 0.0412185 5.512894 0.0415192 0.0265846 0.0000000 0.0010933 0.9989884
chr18 86350490 0.9662702 0.7387057 0.2275645 0.0413510 5.503237 0.0415192 0.0265846 0.0000000 0.0011149 0.9989820
chr18 72044193 0.6732604 0.2751945 0.3980658 0.0966291 4.119523 0.0497032 0.0236148 0.0000380 0.1855471 0.9989811
chr18 35601494 0.6436401 0.9784833 -0.3348432 0.0768366 -4.357862 0.0461787 0.0268136 0.0000131 0.0991910 0.9988799
chr18 72169692 0.6268819 0.9366097 -0.3097278 0.0686921 -4.508929 0.0332414 0.0242311 0.0000065 0.0626075 0.9988678
chr18 54983529 0.8730148 0.4685687 0.4044461 0.0997300 4.055412 0.0417491 0.9894752 0.0000500 0.2235771 0.9988663
chr18 41352385 0.4928893 0.1652186 0.3276707 0.0749252 4.373304 0.0353647 0.0205810 0.0000122 0.0947655 0.9988118
chr18 4461122 0.7227184 0.9841079 -0.2613895 0.0532300 -4.910569 0.0430284 0.0270730 0.0000009 0.0145492 0.9987850
chr18 59394208 0.8843860 0.5200291 0.3643569 0.0872877 4.174205 0.0367941 0.0303132 0.0000299 0.1628116 0.9987715
chr18 39494763 0.7508195 0.9856358 -0.2348163 0.0448626 -5.234125 0.0383424 0.0266343 0.0000002 0.0039837 0.9986725
chr18 72470181 0.2636851 0.5536791 -0.2899940 0.0632559 -4.584461 0.0415192 0.0281403 0.0000046 0.0486359 0.9986659
chr18 22462692 0.9850087 0.7192352 0.2657735 0.0555549 4.783984 0.0417503 0.0265846 0.0000017 0.0230325 0.9985773
chr18 8636264 0.3086341 0.6582554 -0.3496213 0.0838932 -4.167459 0.0415192 0.0265846 0.0000308 0.1644911 0.9985373
chr18 79815488 0.9606927 0.7383977 0.2222950 0.0412334 5.391141 0.0421097 0.0241262 0.0000001 0.0018071 0.9984911
chr18 18693724 0.4695195 0.8035945 -0.3340749 0.0790047 -4.228543 0.0446631 0.0265846 0.0000235 0.1407056 0.9984757
chr18 51282073 0.6553955 0.3515626 0.3038329 0.0688641 4.412068 0.0390713 0.0238350 0.0000102 0.0858812 0.9984615
chr18 73444505 0.1190599 0.3349232 -0.2158633 0.0393250 -5.489216 0.0415192 0.0265846 0.0000000 0.0011484 0.9983920
chr18 29383221 0.9706798 0.7051067 0.2655730 0.0564038 4.708420 0.0415192 0.0265846 0.0000025 0.0305231 0.9983349
chr18 54849907 0.7626734 0.3836918 0.3789816 0.0958679 3.953164 0.0440284 0.0227863 0.0000771 0.2851439 0.9981935
chr18 26619314 0.1445599 0.5849468 -0.4403870 0.1169861 -3.764439 0.0426301 0.0357543 0.0001669 0.4598115 0.9981927
chr18 8965179 0.8158872 0.4413740 0.3745132 0.0946565 3.956548 0.0545744 0.0261612 0.0000760 0.2851439 0.9981350
chr18 17884478 0.9462472 0.6513858 0.2948615 0.0672198 4.386529 0.0411019 0.0247588 0.0000115 0.0917334 0.9981275
chr18 29011712 0.9736893 0.7690227 0.2046666 0.0361406 5.663067 0.0415192 0.0265846 0.0000000 0.0005757 0.9981108
chr18 56460416 0.7124685 0.9607878 -0.2483193 0.0514256 -4.828713 0.0517949 0.0269923 0.0000014 0.0191539 0.9980377
chr18 79602444 0.7093100 0.3677977 0.3415123 0.0838532 4.072737 0.0382452 0.0276370 0.0000465 0.2130363 0.9980128
chr18 87944360 0.7848684 0.5024538 0.2824146 0.0634596 4.450306 0.0415192 0.0249688 0.0000086 0.0761268 0.9979767
chr18 51079162 0.2965761 0.6958993 -0.3993231 0.1043105 -3.828216 0.0330685 0.0212454 0.0001291 0.4024837 0.9979455
chr18 90069436 0.9818616 0.6670851 0.3147765 0.0749035 4.202427 0.0416511 0.0257157 0.0000264 0.1515308 0.9979306
chr18 22627106 0.7133156 0.9799193 -0.2666037 0.0581936 -4.581323 0.0341155 0.0268005 0.0000046 0.0486359 0.9979012
chr18 20144815 0.2275428 0.6214426 -0.3938998 0.1031218 -3.819754 0.0368375 0.0263896 0.0001336 0.4082771 0.9978151
chr18 63615191 0.7036187 0.3798692 0.3237495 0.0785756 4.120229 0.0376622 0.0208463 0.0000378 0.1855471 0.9977973
chr18 39440898 0.8101954 0.4713326 0.3388628 0.0841177 4.028436 0.0300278 0.0318031 0.0000561 0.2393356 0.9977418
chr18 8331514 0.5959395 0.2739571 0.3219824 0.0784654 4.103496 0.0333082 0.0184431 0.0000407 0.1915699 0.9976657
chr18 85448172 0.9728425 0.5493923 0.4234502 0.1145311 3.697251 0.0421529 0.0268694 0.0002179 0.5473555 0.9976319
chr18 59394209 0.8843860 0.5200291 0.3643569 0.0937346 3.887112 0.0370843 0.0229110 0.0001014 0.3457133 0.9976012
chr18 22638440 0.9738574 0.5894693 0.3843882 0.1008620 3.811032 0.0419311 0.0248249 0.0001384 0.4121596 0.9975964
chr18 51034616 0.7783227 0.9764705 -0.1981479 0.0348805 -5.680760 0.0415192 0.0265846 0.0000000 0.0005497 0.9975522
chr18 70340883 0.9849617 0.7107520 0.2742097 0.0622014 4.408417 0.0416285 0.0273169 0.0000104 0.0858812 0.9974507
chr18 14594444 0.9072275 0.5778898 0.3293377 0.0821570 4.008636 0.0364983 0.0207116 0.0000611 0.2531474 0.9973765
chr18 82292682 0.6840182 0.9582598 -0.2742416 0.0624655 -4.390287 0.0415192 0.0265846 0.0000113 0.0912049 0.9973597
chr18 31248397 0.3675608 0.7427996 -0.3752388 0.0988341 -3.796653 0.0369330 0.0284721 0.0001467 0.4267736 0.9973232
chr18 22102017 0.9025752 0.5668629 0.3357122 0.0847738 3.960095 0.0415192 0.0265846 0.0000749 0.2851439 0.9972863
chr18 64629232 0.8479808 0.6207903 0.2271905 0.0458865 4.951138 0.0390249 0.0265846 0.0000007 0.0123902 0.9972130
chr18 36879860 0.7989477 0.5055561 0.2933916 0.0698163 4.202334 0.0508727 0.0248133 0.0000264 0.1515308 0.9971972
chr18 51221363 0.9693148 0.6901257 0.2791892 0.0647235 4.313565 0.0415192 0.0265846 0.0000161 0.1138851 0.9971845
chr18 10216799 0.5380076 0.9020787 -0.3640711 0.0954099 -3.815861 0.0417817 0.0243590 0.0001357 0.4092836 0.9971784
chr18 19187419 0.9021288 0.5933538 0.3087750 0.0756540 4.081409 0.0477153 0.0237557 0.0000448 0.2059183 0.9971064
chr18 42284659 0.7565171 0.3721742 0.3843429 0.1033414 3.719156 0.0308386 0.0218748 0.0001999 0.5227274 0.9970351
chr18 14594443 0.9072275 0.5778898 0.3293377 0.0835125 3.943574 0.0375707 0.0241188 0.0000803 0.2921460 0.9969852
chr18 87623435 0.5946804 0.9352656 -0.3405851 0.0877635 -3.880715 0.0309118 0.0279377 0.0001041 0.3506469 0.9969403
chr18 8285870 0.8175818 0.4998637 0.3177181 0.0795484 3.994023 0.0415192 0.0285179 0.0000650 0.2594437 0.9968993
chr18 10052104 0.7327747 0.4656410 0.2671338 0.0610775 4.373686 0.0380673 0.0249688 0.0000122 0.0947655 0.9968944
chr18 10052100 0.7327747 0.4656410 0.2671338 0.0610787 4.373599 0.0355117 0.0282170 0.0000122 0.0947655 0.9968939
chr18 62858779 0.9817661 0.7251615 0.2566046 0.0572731 4.480373 0.0421342 0.0284870 0.0000075 0.0691510 0.9968748
chr18 3670143 0.3060502 0.6513275 -0.3452773 0.0898504 -3.842802 0.0354165 0.0213125 0.0001216 0.3903282 0.9968321
chr18 69776641 0.7525882 0.9768325 -0.2242444 0.0455833 -4.919443 0.0511767 0.0265846 0.0000009 0.0140665 0.9967913
chr18 88515050 0.9847817 0.7248503 0.2599314 0.0587914 4.421245 0.0415981 0.0272522 0.0000098 0.0834807 0.9967390
chr18 15728999 0.7069291 0.9183028 -0.2113737 0.0409769 -5.158363 0.0415192 0.0283623 0.0000002 0.0051826 0.9967157
chr18 8915110 0.7843213 0.5594167 0.2249046 0.0459948 4.889786 0.0415192 0.0265846 0.0000010 0.0159889 0.9966925
chr18 3202301 0.4335815 0.8082433 -0.3746618 0.1013693 -3.696008 0.0451046 0.0219466 0.0002190 0.5481909 0.9966323
chr18 3202302 0.4335815 0.8082433 -0.3746618 0.1014793 -3.692004 0.0385008 0.0306967 0.0002225 0.5547785 0.9966024
chr18 35567555 0.7626270 0.9348853 -0.1722583 0.0267018 -6.451197 0.0415192 0.0265846 0.0000000 0.0000129 0.9965963
chr18 29293110 0.8556365 0.5110440 0.3445925 0.0904817 3.808421 0.0419818 0.0236148 0.0001399 0.4156467 0.9965669
chr18 67185955 0.9220283 0.6780946 0.2439338 0.0532457 4.581282 0.0397270 0.0265846 0.0000046 0.0486359 0.9965662
chr18 51376197 0.9889372 0.7249662 0.2639709 0.0606733 4.350695 0.0429757 0.0319608 0.0000136 0.1016954 0.9965592
chr18 59841553 0.9709460 0.6649684 0.3059776 0.0763494 4.007596 0.0415192 0.0243227 0.0000613 0.2531474 0.9965104
chr18 52998735 0.5901082 0.9234123 -0.3333041 0.0868360 -3.838318 0.0407498 0.0274143 0.0001239 0.3940112 0.9963924
chr18 7803010 0.6931439 0.9597383 -0.2665943 0.0620637 -4.295493 0.0415192 0.0265846 0.0000174 0.1179388 0.9963653
chr18 85412027 0.9367115 0.6638569 0.2728546 0.0645457 4.227309 0.0426715 0.0255420 0.0000237 0.1408744 0.9962971
chr18 17786157 0.7602678 0.9527978 -0.1925301 0.0346328 -5.559189 0.0415192 0.0265846 0.0000000 0.0008995 0.9962272
chr18 33788006 0.9147396 0.4992388 0.4155007 0.1182925 3.512486 0.0422440 0.0265846 0.0004439 0.8272376 0.9961814
chr18 63482434 0.9030487 0.6129989 0.2900498 0.0717040 4.045101 0.0382897 0.0258520 0.0000523 0.2278085 0.9959811
chr18 73692036 0.9451192 0.4325410 0.5125783 0.1558781 3.288328 0.0415192 0.0249688 0.0010078 0.9999991 0.9959796
chr18 73692051 0.9451192 0.4325410 0.5125783 0.1559275 3.287287 0.0415192 0.0280145 0.0010116 0.9999991 0.9959698
chr18 65930744 0.5382777 0.2871105 0.2511672 0.0570548 4.402209 0.0415192 0.0265846 0.0000107 0.0878565 0.9959695
chr18 61321824 0.9421764 0.6362593 0.3059171 0.0778257 3.930800 0.0437148 0.0265846 0.0000847 0.3030617 0.9959261
chr18 90133658 0.9219964 0.6362605 0.2857358 0.0702078 4.069861 0.0375451 0.0181373 0.0000470 0.2149763 0.9959217
chr18 52517228 0.4970581 0.8064482 -0.3093902 0.0791967 -3.906606 0.0693750 0.0229465 0.0000936 0.3253511 0.9959026
chr18 22638439 0.9738574 0.5894693 0.3843882 0.1076870 3.569495 0.0417351 0.0229477 0.0003577 0.7374780 0.9958688
chr18 10052050 0.7564003 0.4771996 0.2792006 0.0678696 4.113783 0.0419064 0.0370396 0.0000389 0.1883234 0.9958592
chr18 24060026 0.8756257 0.6338014 0.2418243 0.0538052 4.494440 0.0415192 0.0265846 0.0000070 0.0652517 0.9958041
chr18 10052099 0.7327747 0.4656410 0.2671338 0.0634866 4.207717 0.0504884 0.0308046 0.0000258 0.1504435 0.9957631
chr18 85865147 0.4486464 0.7812474 -0.3326010 0.0887191 -3.748924 0.0420595 0.0223678 0.0001776 0.4778739 0.9956268
chr18 18010044 0.5305020 0.8481402 -0.3176382 0.0833038 -3.813010 0.0463314 0.0234995 0.0001373 0.4115102 0.9955072
chr18 26028885 0.8337710 0.4589697 0.3748013 0.1061090 3.532230 0.0350516 0.0265846 0.0004121 0.8123910 0.9952023
chr18 10052221 0.6371979 0.3869461 0.2502518 0.0581590 4.302890 0.0415192 0.0265846 0.0000169 0.1161540 0.9951093
chr18 10052074 0.7403147 0.4704809 0.2698338 0.0657437 4.104330 0.0356412 0.0423386 0.0000405 0.1915699 0.9951066
chr18 40714756 0.4390751 0.8278898 -0.3888147 0.1119321 -3.473666 0.0380361 0.0241872 0.0005134 0.8780332 0.9950701
chr18 43423206 0.9204154 0.6061048 0.3143106 0.0830654 3.783895 0.0440272 0.0319787 0.0001544 0.4373853 0.9950606
chr18 8481767 0.7234858 0.9826656 -0.2591798 0.0617156 -4.199586 0.0413833 0.0269411 0.0000267 0.1521298 0.9950492
chr18 10052144 0.7279823 0.4710140 0.2569683 0.0609961 4.212867 0.0415192 0.0249688 0.0000252 0.1488150 0.9949650
chr18 10052149 0.7279823 0.4710140 0.2569683 0.0609961 4.212867 0.0415192 0.0249688 0.0000252 0.1488150 0.9949650
chr18 10052103 0.7327747 0.4656410 0.2671338 0.0650030 4.109558 0.0399561 0.0297370 0.0000396 0.1898341 0.9949322
chr18 17907723 0.9738741 0.6614956 0.3123785 0.0826314 3.780384 0.0415192 0.0265846 0.0001566 0.4402395 0.9949182
chr18 85814206 0.8936719 0.6879358 0.2057362 0.0411601 4.998443 0.0415192 0.0265846 0.0000006 0.0103278 0.9948989
chr18 23066200 0.2394678 0.5794266 -0.3399588 0.0934686 -3.637145 0.0453596 0.0249102 0.0002757 0.6330298 0.9948761
chr18 10051989 0.7566729 0.4786114 0.2780615 0.0693831 4.007624 0.0393010 0.0286368 0.0000613 0.2531474 0.9948613
chr18 85077515 0.9686480 0.7243753 0.2442727 0.0563353 4.336050 0.0415192 0.0265846 0.0000145 0.1064205 0.9947809
chr18 33768529 0.9490765 0.6679561 0.2811203 0.0709676 3.961247 0.0329722 0.0240894 0.0000746 0.2851439 0.9946471
chr18 62698279 0.5904027 0.9512146 -0.3608118 0.1022596 -3.528389 0.0339402 0.0266784 0.0004181 0.8133174 0.9946247
chr18 51667413 0.6849978 0.9286454 -0.2436477 0.0563554 -4.323415 0.0390249 0.0267223 0.0000154 0.1103809 0.9945978
chr18 10052206 0.6371979 0.3869461 0.2502518 0.0590864 4.235355 0.0415192 0.0277433 0.0000228 0.1388131 0.9945034
chr18 10052177 0.6678399 0.4112901 0.2565497 0.0615919 4.165319 0.0415192 0.0278752 0.0000311 0.1654077 0.9944847
chr18 9617108 0.8484580 0.5729463 0.2755117 0.0690559 3.989690 0.0537413 0.0181404 0.0000662 0.2634740 0.9944825
chr18 10052013 0.7564003 0.4771996 0.2792006 0.0705372 3.958203 0.0408236 0.0281653 0.0000755 0.2851439 0.9944655
chr18 90338779 0.4796450 0.8032306 -0.3235856 0.0880584 -3.674670 0.0354419 0.0215772 0.0002382 0.5763071 0.9944432
chr18 7599628 0.9446094 0.7028276 0.2417818 0.0558558 4.328677 0.0359331 0.0240040 0.0000150 0.1088993 0.9944312
chr18 10052139 0.7279823 0.4710140 0.2569683 0.0618499 4.154711 0.0415192 0.0248401 0.0000326 0.1706662 0.9944239
chr18 20144814 0.2275428 0.6214426 -0.3938998 0.1158552 -3.399932 0.0353472 0.0266302 0.0006740 0.9999991 0.9944163
chr18 10052172 0.6863975 0.4321308 0.2542667 0.0608561 4.178163 0.0415192 0.0279998 0.0000294 0.1612646 0.9943767
chr18 3441115 0.6202424 0.8750680 -0.2548256 0.0611125 -4.169780 0.0313167 0.0245764 0.0000305 0.1634514 0.9943528
chr18 43086637 0.4163586 0.7157860 -0.2994274 0.0787291 -3.803261 0.0467283 0.0238907 0.0001428 0.4208154 0.9943470
chr18 90133659 0.9219964 0.6362605 0.2857358 0.0736182 3.881322 0.0374288 0.0194441 0.0001039 0.3506203 0.9941815
chr18 10052116 0.7279823 0.4710140 0.2569683 0.0622732 4.126465 0.0390523 0.0248401 0.0000368 0.1833805 0.9941429
chr18 52517227 0.4970581 0.8064482 -0.3093902 0.0830914 -3.723493 0.0384074 0.0187918 0.0001965 0.5167342 0.9941327
chr18 40714755 0.4390751 0.8278898 -0.3888147 0.1146751 -3.390575 0.0447521 0.0288675 0.0006975 0.9999991 0.9941181
chr18 90041206 0.1805662 0.5061890 -0.3256228 0.0896074 -3.633882 0.0431780 0.0249275 0.0002792 0.6379399 0.9940982
chr18 10052135 0.7279823 0.4710140 0.2569683 0.0623827 4.119221 0.0415192 0.0248401 0.0000380 0.1855471 0.9940688
chr18 8331513 0.5959395 0.2739571 0.3219824 0.0883188 3.645682 0.0299910 0.0197204 0.0002667 0.6200831 0.9940226
chr18 19187420 0.9021288 0.5933538 0.3087750 0.0831199 3.714814 0.0445726 0.0206193 0.0002034 0.5268429 0.9939934
chr18 68364829 0.9336776 0.6362128 0.2974648 0.0786238 3.783396 0.0351931 0.0215377 0.0001547 0.4373853 0.9939895
chr18 3358343 0.9850959 0.6992617 0.2858341 0.0742330 3.850497 0.0425878 0.0216385 0.0001179 0.3821005 0.9938496
chr18 83697833 0.8853226 0.5805762 0.3047464 0.0818016 3.725435 0.0422421 0.0201486 0.0001950 0.5137406 0.9938425
chr18 33768528 0.9490765 0.6679561 0.2811203 0.0723810 3.883897 0.0425705 0.0213771 0.0001028 0.3490797 0.9938309
chr18 9438090 0.9359379 0.7766550 0.1592829 0.0237192 6.715359 0.0415192 0.0265846 0.0000000 0.0000033 0.9937792
chr18 14397495 0.7668246 0.9717626 -0.2049380 0.0419957 -4.879982 0.0415192 0.0265846 0.0000011 0.0164311 0.9937690
chr18 18781316 0.7348971 0.9808761 -0.2459790 0.0584457 -4.208673 0.0341486 0.0267888 0.0000257 0.1504376 0.9937496
chr18 89134557 0.9864468 0.7382886 0.2481582 0.0593196 4.183412 0.0424214 0.0213630 0.0000287 0.1588351 0.9937486
chr18 52895306 0.9800047 0.6523109 0.3276938 0.0912062 3.592889 0.0424797 0.0207145 0.0003270 0.6980552 0.9937296
chr18 72169693 0.6268819 0.9366097 -0.3097278 0.0840202 -3.686347 0.0457618 0.0288339 0.0002275 0.5612256 0.9937232
chr18 10052125 0.7279823 0.4710140 0.2569683 0.0629127 4.084525 0.0425065 0.0248401 0.0000442 0.2038469 0.9937025
chr18 3670142 0.3060502 0.6513275 -0.3452773 0.0983372 -3.511155 0.0479941 0.0214941 0.0004462 0.8288784 0.9936917
chr18 20133750 0.9898095 0.7171429 0.2726666 0.0692480 3.937540 0.0423330 0.2036026 0.0000823 0.2972600 0.9936747
chr18 3131496 0.7612499 0.9838771 -0.2226271 0.0492176 -4.523321 0.0423866 0.0268314 0.0000061 0.0593373 0.9936403
chr18 27029408 0.9718312 0.7044817 0.2673495 0.0672081 3.977938 0.0415192 0.0316702 0.0000695 0.2728157 0.9936133
chr18 24787917 0.4289203 0.1548270 0.2740933 0.0699834 3.916546 0.0365223 0.0265846 0.0000898 0.3177759 0.9935703
chr18 52198885 0.7874982 0.5003396 0.2871587 0.0753280 3.812110 0.0387835 0.0284957 0.0001378 0.4121258 0.9935150
chr18 89544067 0.9380497 0.4944328 0.4436169 0.1388525 3.194878 0.0355764 0.0277403 0.0013989 0.9999991 0.9933776
chr18 37527276 0.6361135 0.8799111 -0.2437975 0.0580512 -4.199696 0.0415192 0.0265846 0.0000267 0.1521298 0.9933769
chr18 10051981 0.7713326 0.5076365 0.2636961 0.0661060 3.988991 0.0321884 0.0248324 0.0000664 0.2634987 0.9933618
chr18 10052148 0.7279823 0.4710140 0.2569683 0.0634459 4.050194 0.0498529 0.0248401 0.0000512 0.2253554 0.9933204
chr18 10052134 0.7279823 0.4710140 0.2569683 0.0634471 4.050117 0.0390249 0.0323713 0.0000512 0.2253554 0.9933196
chr18 10052138 0.7279823 0.4710140 0.2569683 0.0634471 4.050117 0.0390249 0.0323713 0.0000512 0.2253554 0.9933196
chr18 10052143 0.7279823 0.4710140 0.2569683 0.0634515 4.049841 0.0425065 0.0323713 0.0000513 0.2253554 0.9933164
chr18 27942200 0.9718312 0.6594683 0.3123629 0.0859051 3.636137 0.0415192 0.0305460 0.0002768 0.6344650 0.9932840
chr18 32993960 0.5542468 0.9088841 -0.3546373 0.1031161 -3.439205 0.0409582 0.0276059 0.0005834 0.9455829 0.9932387
chr18 49620049 0.6648600 0.9261426 -0.2612825 0.0653216 -3.999940 0.0340056 0.0238658 0.0000634 0.2567198 0.9932265
chr18 41819191 0.7334878 0.4230172 0.3104705 0.0854319 3.634129 0.0322257 0.0250376 0.0002789 0.6379399 0.9931234
chr18 66616017 0.8125584 0.4389725 0.3735859 0.1113430 3.355272 0.0424020 0.0207831 0.0007929 0.9999991 0.9930082
chr18 3236959 0.6936342 0.9863807 -0.2927465 0.0784417 -3.732029 0.0383360 0.0274255 0.0001899 0.5033288 0.9929990
chr18 10052124 0.7279823 0.4710140 0.2569683 0.0639680 4.017140 0.0427340 0.0323713 0.0000589 0.2473169 0.9929334
chr18 8791414 0.9856789 0.7552087 0.2304702 0.0532284 4.329839 0.0418810 0.0211255 0.0000149 0.1088936 0.9928798
chr18 88230118 0.9087590 0.6296544 0.2791046 0.0731363 3.816226 0.0378690 0.0222390 0.0001355 0.4092836 0.9928358
chr18 29288185 0.9465243 0.6479676 0.2985567 0.0810847 3.682033 0.0362895 0.0250851 0.0002314 0.5672271 0.9928329
chr18 33629767 0.9834459 0.7058934 0.2775525 0.0726226 3.821848 0.0417587 0.0288577 0.0001325 0.4066557 0.9927548
chr18 3358344 0.9850959 0.6992617 0.2858341 0.0760743 3.757302 0.0417160 0.0215259 0.0001718 0.4694103 0.9927132
chr18 48906205 0.9862158 0.7208906 0.2653253 0.0676838 3.920070 0.0420633 0.0274519 0.0000885 0.3139628 0.9927093
chr18 32993959 0.5542468 0.9088841 -0.3546373 0.1043068 -3.399945 0.0626200 0.0243002 0.0006740 0.9999991 0.9926880
chr18 10052176 0.6678399 0.4112901 0.2565497 0.0641277 4.000604 0.0415192 0.0293749 0.0000632 0.2567198 0.9926811
chr18 26499750 0.9004923 0.5984799 0.3020125 0.0827545 3.649501 0.0373464 0.9894752 0.0002628 0.6165523 0.9926794
chr18 10052049 0.7564003 0.4771996 0.2792006 0.0734640 3.800507 0.0416502 0.0281231 0.0001444 0.4228374 0.9926422
chr18 10052245 0.5950548 0.3569856 0.2380691 0.0566106 4.205382 0.0415192 0.0265846 0.0000261 0.1507439 0.9926345
chr18 10052220 0.6371979 0.3869461 0.2502518 0.0616299 4.060556 0.0390249 0.0277433 0.0000490 0.2208308 0.9926150
chr18 45307674 0.9634430 0.7236613 0.2397817 0.0573718 4.179432 0.0309617 0.0213060 0.0000292 0.1610008 0.9925832
chr18 30722919 0.9857162 0.7003973 0.2853189 0.0760627 3.751102 0.0421825 0.0243406 0.0001761 0.4764352 0.9925830
chr18 29652024 0.9695319 0.6873749 0.2821570 0.0747709 3.773622 0.0416083 0.0266653 0.0001609 0.4485226 0.9925790
chr18 63615192 0.7036187 0.3798692 0.3237495 0.0920090 3.518671 0.0288531 0.0232906 0.0004337 0.8252523 0.9924905
chr18 10052073 0.7431373 0.4734167 0.2697206 0.0698195 3.863110 0.0543355 0.0400620 0.0001120 0.3662996 0.9924683
chr18 37149984 0.5403387 0.8969394 -0.3566007 0.1056326 -3.375859 0.0372821 0.0271914 0.0007359 0.9999991 0.9924412
chr18 27756749 0.9880580 0.7441493 0.2439087 0.0592400 4.117295 0.0424773 0.0231950 0.0000383 0.1861749 0.9924349
chr18 19871761 0.9796952 0.7118462 0.2678490 0.0691114 3.875612 0.0418899 0.0292260 0.0001064 0.3546517 0.9924230
chr18 37290274 0.4612712 0.7702699 -0.3089987 0.0860591 -3.590540 0.0346345 0.0376733 0.0003300 0.7000888 0.9924213
chr18 10052152 0.7083110 0.4634366 0.2448745 0.0596779 4.103271 0.0415192 0.0249688 0.0000407 0.1915699 0.9924006
chr18 10052154 0.7083110 0.4634366 0.2448745 0.0596779 4.103271 0.0415192 0.0249688 0.0000407 0.1915699 0.9924006
chr18 50541503 0.6958351 0.9608848 -0.2650497 0.0680870 -3.892807 0.0394367 0.0265846 0.0000991 0.3393541 0.9923268
chr18 8814171 0.9397416 0.5893603 0.3503814 0.1033296 3.390910 0.0386354 0.0214216 0.0006966 0.9999991 0.9923129
chr18 40502627 0.9306689 0.6307912 0.2998777 0.0825487 3.632739 0.0488481 0.9894752 0.0002804 0.6386814 0.9922688
chr18 7959028 0.6700175 0.9782323 -0.3082148 0.0860306 -3.582618 0.0390528 0.0266262 0.0003402 0.7119212 0.9922459
chr18 10052151 0.7193899 0.4669705 0.2524195 0.0629881 4.007414 0.0390249 0.0322538 0.0000614 0.2531474 0.9922358
chr18 70790585 0.7558363 0.9599903 -0.2041540 0.0430428 -4.743044 0.0415192 0.0265846 0.0000021 0.0274248 0.9922350
chr18 63485784 0.8764124 0.5286457 0.3477667 0.1024561 3.394300 0.0934580 0.0236880 0.0006880 0.9999991 0.9922090
chr18 10052171 0.6863975 0.4321308 0.2542667 0.0638394 3.982912 0.0390249 0.0296696 0.0000681 0.2682628 0.9921644
chr18 10052115 0.7279823 0.4710140 0.2569683 0.0649616 3.955696 0.0369000 0.0323713 0.0000763 0.2851439 0.9921610
chr18 52687734 0.5678640 0.8308040 -0.2629400 0.0674783 -3.896660 0.0452086 0.0265846 0.0000975 0.3356512 0.9921260
chr18 51422779 0.9300298 0.6253027 0.3047272 0.0848961 3.589411 0.0441144 0.0244330 0.0003314 0.7020572 0.9920574
chr18 40403128 0.7349264 0.9774212 -0.2424948 0.0591049 -4.102790 0.0390249 0.0265846 0.0000408 0.1915699 0.9920430
chr18 9629443 0.7250295 0.9530200 -0.2279905 0.0530935 -4.294129 0.0415192 0.0267675 0.0000175 0.1180929 0.9920382
chr18 73834917 0.9598879 0.7470190 0.2128690 0.0468692 4.541766 0.0441888 0.0240647 0.0000056 0.0555394 0.9919836
chr18 19871762 0.9796952 0.7118462 0.2678490 0.0698009 3.837330 0.0419984 0.0218622 0.0001244 0.3940112 0.9919068
chr18 53622854 0.7760276 0.9751060 -0.1990784 0.0412084 -4.831019 0.0423202 0.0265846 0.0000014 0.0191539 0.9918989
chr18 22436774 0.6984364 0.9711462 -0.2727098 0.0718976 -3.793032 0.0415192 0.0265846 0.0001488 0.4294617 0.9918509
chr18 43423207 0.9204154 0.6061048 0.3143106 0.0892442 3.521916 0.0406376 0.0303837 0.0004284 0.8190080 0.9918354
chr18 63330711 0.6696503 0.9254095 -0.2557592 0.0649366 -3.938602 0.0379905 0.0267306 0.0000820 0.2967171 0.9917719
chr18 10052239 0.6052774 0.3661802 0.2390972 0.0580210 4.120877 0.0390249 0.0265846 0.0000377 0.1855471 0.9917432
chr18 31567248 0.5839903 0.0592138 0.5247765 0.1779741 2.948612 0.0375202 0.0290269 0.0031920 0.9999991 0.9917242
chr18 10052240 0.5950548 0.3569856 0.2380691 0.0576251 4.131344 0.0415192 0.0265846 0.0000361 0.1801742 0.9917122
chr18 89743744 0.6636934 0.9606512 -0.2969578 0.0822474 -3.610544 0.0369330 0.0267366 0.0003056 0.6675477 0.9916837
chr18 10967245 0.4686354 0.8767019 -0.4080665 0.1287785 -3.168747 0.0496976 0.0190914 0.0015310 0.9999991 0.9916664
chr18 37459939 0.1952729 0.3987973 -0.2035244 0.0432457 -4.706229 0.0415192 0.0265846 0.0000025 0.0305845 0.9916640
chr18 86000985 0.9392838 0.6918537 0.2474302 0.0616184 4.015524 0.0368847 0.0267005 0.0000593 0.2482702 0.9916360
chr18 10052233 0.6181545 0.3778494 0.2403051 0.0586444 4.097665 0.0415192 0.0265846 0.0000417 0.1952025 0.9916324
chr18 34092830 0.4318150 0.6836908 -0.2518758 0.0635373 -3.964216 0.0415192 0.0265846 0.0000736 0.2831618 0.9915836
chr18 23066201 0.2394678 0.5794266 -0.3399588 0.1005811 -3.379948 0.0567585 0.0333163 0.0007250 0.9999991 0.9914834
chr18 76709814 0.7433468 0.9600270 -0.2166802 0.0489262 -4.428711 0.0335097 0.0282363 0.0000095 0.0823512 0.9914562
chr18 24336880 0.5007355 0.8016270 -0.3008914 0.0842715 -3.570501 0.0337384 0.0255957 0.0003563 0.7365765 0.9914349
chr18 18905411 0.8058938 0.5359603 0.2699335 0.0712924 3.786287 0.0415192 0.0265846 0.0001529 0.4358667 0.9914283
chr18 50592323 0.7675902 0.5086723 0.2589179 0.0667908 3.876549 0.0415192 0.0265846 0.0001059 0.3546517 0.9913281
chr18 37362011 0.5138466 0.7760141 -0.2621675 0.0682001 -3.844093 0.0413220 0.0265846 0.0001210 0.3903282 0.9912924
chr18 63248781 0.6255764 0.8763968 -0.2508204 0.0634474 -3.953200 0.0403654 0.0273233 0.0000771 0.2851439 0.9912752
chr18 68364828 0.9336776 0.6362128 0.2974648 0.0831713 3.576534 0.0352944 0.0209125 0.0003482 0.7232596 0.9912073
chr18 10052205 0.6371979 0.3869461 0.2502518 0.0632947 3.953756 0.0406071 0.0290686 0.0000769 0.2851439 0.9911980
chr18 85814243 0.8936719 0.6879358 0.2057362 0.0446632 4.606389 0.0415192 0.0265846 0.0000041 0.0446160 0.9910435
chr18 26774028 0.7667838 0.4676012 0.2991826 0.0842222 3.552301 0.0401830 0.0252468 0.0003819 0.7736579 0.9909852
chr18 72044192 0.6732604 0.2751945 0.3980658 0.1262713 3.152466 0.0361443 0.0288312 0.0016190 0.9999991 0.9909153
chr18 29389655 0.8657386 0.6701410 0.1955977 0.0404929 4.830414 0.0415192 0.0265846 0.0000014 0.0191539 0.9908834
chr18 24311621 0.8646754 0.5391645 0.3255109 0.0955854 3.405444 0.0347309 0.0271214 0.0006606 0.9999991 0.9908485
chr18 10052246 0.5950548 0.3569856 0.2380691 0.0586221 4.061084 0.0415192 0.0265846 0.0000488 0.2208308 0.9907447
chr18 10052232 0.6181545 0.3778494 0.2403051 0.0595759 4.033594 0.0390249 0.0265846 0.0000549 0.2355809 0.9907402
chr18 48994376 0.6643638 0.8939254 -0.2295616 0.0550170 -4.172556 0.0415192 0.0265846 0.0000301 0.1633567 0.9907371
chr18 38214280 0.6222479 0.2914899 0.3307579 0.0980672 3.372769 0.0390249 0.0244477 0.0007442 0.9999991 0.9906958
chr18 10052012 0.7564003 0.4771996 0.2792006 0.0763129 3.658628 0.0328097 0.0193738 0.0002536 0.6010801 0.9905690
chr18 10216800 0.5380076 0.9020787 -0.3640711 0.1125071 -3.235982 0.0377086 0.0231290 0.0012122 0.9999991 0.9905597
chr18 34092829 0.4318150 0.6836908 -0.2518758 0.0647385 -3.890665 0.0415192 0.0265846 0.0001000 0.3415237 0.9905117
chr18 85677298 0.9455441 0.6210509 0.3244932 0.0957129 3.390277 0.0428684 0.0265846 0.0006982 0.9999991 0.9905034
chr18 89978487 0.9813749 0.7276510 0.2537240 0.0655709 3.869460 0.0421550 0.0311452 0.0001091 0.3613709 0.9904710
chr18 28212707 0.9803191 0.7607030 0.2196161 0.0510483 4.302125 0.0415674 0.0351458 0.0000169 0.1161540 0.9904403
chr18 28755875 0.9810817 0.7761729 0.2049088 0.0447736 4.576550 0.0415192 0.0265846 0.0000047 0.0489650 0.9904377
chr18 59986422 0.9191558 0.6964245 0.2227313 0.0523963 4.250895 0.0372243 0.0272175 0.0000213 0.1342867 0.9904190
chr18 52337196 0.7854786 0.9808738 -0.1953952 0.0407783 -4.791650 0.0422164 0.0267215 0.0000017 0.0223847 0.9903417
chr18 43128686 0.8057276 0.9747641 -0.1690365 0.0295195 -5.726259 0.0415192 0.0265846 0.0000000 0.0004616 0.9903238
chr18 80205218 0.4990469 0.8488508 -0.3498039 0.1068813 -3.272827 0.0314533 0.0230309 0.0010648 0.9999991 0.9902987
chr18 45990773 0.9890135 0.7461772 0.2428363 0.0611379 3.971943 0.0427391 0.0214894 0.0000713 0.2765788 0.9902621
chr18 10051988 0.7578451 0.4790925 0.2787527 0.0765434 3.641758 0.0374072 0.0223312 0.0002708 0.6269555 0.9902368
chr18 45881408 0.9461284 0.7055183 0.2406101 0.0602128 3.995997 0.0419623 0.0265846 0.0000644 0.2587744 0.9902340
chr18 23383736 0.9331698 0.7215316 0.2116382 0.0478101 4.426638 0.0418900 0.0249688 0.0000096 0.0823512 0.9902291
chr18 26133424 0.7525463 0.5385492 0.2139971 0.0488499 4.380707 0.0415192 0.0265846 0.0000118 0.0936840 0.9901922
chr18 37451855 0.7517203 0.9743579 -0.2226376 0.0525560 -4.236196 0.0484164 0.0265846 0.0000227 0.1388131 0.9901881
chr18 10052153 0.7083110 0.4634366 0.2448745 0.0621242 3.941689 0.0426106 0.0248035 0.0000809 0.2936853 0.9901500
chr18 54983528 0.8730148 0.4685687 0.4044461 0.1306840 3.094841 0.0422371 0.0217162 0.0019692 0.9999991 0.9901440
chr18 82292665 0.6840182 0.9582598 -0.2742416 0.0747533 -3.668625 0.0415192 0.0268186 0.0002439 0.5858290 0.9901207
chr18 18010045 0.5305020 0.8481402 -0.3176382 0.0935613 -3.394974 0.0323117 0.0194299 0.0006864 0.9999991 0.9899989
chr18 20517806 0.6070258 0.8894808 -0.2824549 0.0784682 -3.599609 0.0377088 0.0265846 0.0003187 0.6876323 0.9899701
chr18 4289766 0.5577791 0.7746258 -0.2168467 0.0502760 -4.313128 0.0450019 0.0265846 0.0000161 0.1138851 0.9899401
chr18 58650691 0.9311943 0.6614124 0.2697819 0.0731210 3.689524 0.0415192 0.0265846 0.0002247 0.5573609 0.9898818
chr18 88230119 0.9087590 0.6296544 0.2791046 0.0771404 3.618135 0.0311820 0.0209681 0.0002967 0.6565063 0.9898785
chr18 29341880 0.7128295 0.9340700 -0.2212405 0.0522305 -4.235850 0.0610259 0.0198220 0.0000228 0.1388131 0.9898636
chr18 71899519 0.7906614 0.9709459 -0.1802844 0.0345927 -5.211629 0.0415192 0.0265846 0.0000002 0.0044222 0.9898525
chr18 63704010 0.9714953 0.6337320 0.3377633 0.1027102 3.288508 0.0417537 0.0287801 0.0010072 0.9999991 0.9897008
chr18 60936906 0.9038722 0.6007433 0.3031289 0.0877597 3.454078 0.0359832 0.0267665 0.0005522 0.9217314 0.9896849
chr18 28617994 0.9852606 0.7143380 0.2709226 0.0738532 3.668393 0.0417687 0.0213094 0.0002441 0.5858290 0.9896762
chr18 40280076 0.9763277 0.7272101 0.2491176 0.0644673 3.864246 0.0415192 0.0241439 0.0001114 0.3662996 0.9896407
chr18 83729631 0.7323883 0.9851920 -0.2528037 0.0660927 -3.824989 0.0390496 0.0269025 0.0001308 0.4050743 0.9896101
chr18 41065011 0.9065219 0.6548692 0.2516527 0.0656035 3.835965 0.0422842 0.0243566 0.0001251 0.3950686 0.9896017
chr18 59563885 0.7617522 0.9724975 -0.2107453 0.0479404 -4.395986 0.0397447 0.0267347 0.0000110 0.0893604 0.9895576
chr18 23183610 0.9771965 0.6598346 0.3173619 0.0941185 3.371941 0.0418940 0.0263728 0.0007464 0.9999991 0.9895453
chr18 59966022 0.9617732 0.6933223 0.2684509 0.0729366 3.680604 0.0325298 0.0233463 0.0002327 0.5676098 0.9895437
chr18 7959029 0.6700175 0.9782323 -0.3082148 0.0901954 -3.417189 0.0377245 0.0273720 0.0006327 0.9999991 0.9895169
chr18 24808248 0.5373932 0.2825925 0.2548007 0.0670900 3.797891 0.0457211 0.0241673 0.0001459 0.4255357 0.9894826
chr18 23294094 0.7093203 0.9368885 -0.2275682 0.0553391 -4.112249 0.0415192 0.0265846 0.0000392 0.1883234 0.9894226
chr18 52140234 0.7302191 0.4631064 0.2671127 0.0725552 3.681508 0.0483861 0.0281152 0.0002319 0.5672271 0.9893678
chr18 86635639 0.9873329 0.7443337 0.2429993 0.0621187 3.911855 0.0421262 0.0271063 0.0000916 0.3215663 0.9893334
chr18 59966021 0.9617732 0.6933223 0.2684509 0.0731906 3.667834 0.0454593 0.0210309 0.0002446 0.5858290 0.9893196
chr18 25789740 0.9736689 0.7342089 0.2394601 0.0605998 3.951500 0.0415192 0.0265846 0.0000777 0.2863741 0.9893135
chr18 24351848 0.9813096 0.8193825 0.1619271 0.0269127 6.016763 0.0416578 0.0265846 0.0000000 0.0001127 0.9893053
chr18 11142862 0.6160679 0.3459026 0.2701653 0.0741053 3.645692 0.0382909 0.0275486 0.0002667 0.6200831 0.9891698
chr18 25915761 0.8696443 0.5853927 0.2842516 0.0803209 3.538948 0.0384945 0.0280297 0.0004017 0.7991819 0.9891040
chr18 3770286 0.3097341 0.5485716 -0.2388375 0.0605423 -3.944968 0.0378839 0.0265846 0.0000798 0.2917754 0.9890826
chr18 40502626 0.9306689 0.6307912 0.2998777 0.0871929 3.439243 0.0447970 0.0248063 0.0005833 0.9455829 0.9890599
chr18 45313613 0.5623329 0.2219507 0.3403822 0.1049285 3.243943 0.0438031 0.0243836 0.0011789 0.9999991 0.9890293
chr18 9832409 0.3703661 0.6393366 -0.2689705 0.0738992 -3.639692 0.0415192 0.0265846 0.0002730 0.6288727 0.9888877
chr18 47731239 0.8019967 0.4804614 0.3215354 0.0969882 3.315202 0.0380960 0.0238141 0.0009158 0.9999991 0.9888255
chr18 51376196 0.9889372 0.7249662 0.2639709 0.0717932 3.676821 0.0420608 0.0305475 0.0002362 0.5724639 0.9888125
chr18 46315307 0.9820364 0.7008343 0.2812022 0.0794152 3.540911 0.0427064 0.0182359 0.0003987 0.7985495 0.9887475
chr18 54467331 0.9875718 0.7408218 0.2467500 0.0644322 3.829606 0.0428972 0.0415918 0.0001283 0.4012936 0.9886244
chr18 52014321 0.4307128 0.6953565 -0.2646437 0.0723065 -3.660025 0.0381652 0.0218099 0.0002522 0.5988308 0.9886078
chr18 63704009 0.9714953 0.6337320 0.3377633 0.1046398 3.227867 0.0419669 0.0277609 0.0012472 0.9999991 0.9884774
chr18 83609826 0.6110777 0.8826321 -0.2715545 0.0756089 -3.591566 0.0455449 0.0343948 0.0003287 0.6996406 0.9883654
chr18 8638752 0.7780124 0.9854862 -0.2074738 0.0473923 -4.377795 0.0461181 0.0267790 0.0000120 0.0944079 0.9883277
chr18 45990772 0.9890135 0.7461772 0.2428363 0.0630006 3.854507 0.0422556 0.0267550 0.0001160 0.3776496 0.9883117
chr18 11546878 0.1937858 0.4152865 -0.2215007 0.0535925 -4.133057 0.0415192 0.0265846 0.0000358 0.1801273 0.9883086
chr18 88865299 0.7450399 0.9880315 -0.2429916 0.0631215 -3.849588 0.0284369 0.0274637 0.0001183 0.3826324 0.9882541
chr18 85732508 0.9826618 0.7541668 0.2284950 0.0567449 4.026703 0.0416511 0.0236666 0.0000566 0.2403704 0.9882262
chr18 48226310 0.3114464 0.5888854 -0.2774390 0.0784537 -3.536342 0.0415192 0.0310973 0.0004057 0.8032561 0.9881429
chr18 40975782 0.7060331 0.9512414 -0.2452083 0.0642678 -3.815415 0.0372123 0.0275181 0.0001360 0.4092836 0.9880716
chr18 18389146 0.8265674 0.4999322 0.3266352 0.1003333 3.255502 0.1196831 0.0248766 0.0011319 0.9999991 0.9880634
chr18 8965178 0.8158872 0.4413740 0.3745132 0.1217239 3.076743 0.0399422 0.0220477 0.0020928 0.9999991 0.9879884
chr18 63482435 0.9030487 0.6129989 0.2900498 0.0842210 3.443913 0.0323808 0.0259354 0.0005734 0.9379935 0.9879841
chr18 47731240 0.8019967 0.4804614 0.3215354 0.0981931 3.274522 0.0425548 0.0216738 0.0010584 0.9999991 0.9879773
chr18 28292345 0.4052572 0.7084005 -0.3031433 0.0900779 -3.365344 0.0434511 0.0242151 0.0007645 0.9999991 0.9879433
chr18 9091646 0.5213744 0.8018567 -0.2804823 0.0800593 -3.503430 0.0413331 0.0270195 0.0004593 0.8348718 0.9879141
chr18 16327886 0.7921129 0.5290478 0.2630651 0.0724142 3.632781 0.0415192 0.0265846 0.0002804 0.6386814 0.9878340
chr18 90338778 0.4796450 0.8032306 -0.3235856 0.0994285 -3.254454 0.0314696 0.0216002 0.0011361 0.9999991 0.9877446
chr18 63485783 0.8764124 0.5286457 0.3477667 0.1104384 3.148966 0.0336192 0.0339214 0.0016385 0.9999991 0.9875923
chr18 36905930 0.6188598 0.8932446 -0.2743848 0.0777234 -3.530273 0.0356428 0.0244319 0.0004151 0.8133174 0.9875736
chr18 70203505 0.8256504 0.9798424 -0.1541920 0.0241723 -6.378870 0.0415192 0.0265846 0.0000000 0.0000178 0.9875162
chr18 10051950 0.7994371 0.5629016 0.2365355 0.0609265 3.882310 0.0374843 0.0239843 0.0001035 0.3500460 0.9874866
chr18 6572039 0.6199008 0.9192658 -0.2993649 0.0889677 -3.364872 0.0303413 0.0225066 0.0007658 0.9999991 0.9874863
chr18 49829224 0.9291608 0.7757088 0.1534519 0.0239070 6.418712 0.0415192 0.0265846 0.0000000 0.0000147 0.9873186
chr18 38757536 0.7488914 0.9126372 -0.1637458 0.0285485 -5.735710 0.0415192 0.0265846 0.0000000 0.0004512 0.9872221
chr18 8746574 0.8981924 0.6249870 0.2732054 0.0775798 3.521606 0.0421491 0.0249688 0.0004289 0.8190080 0.9872134
chr18 79840767 0.8970423 0.6417094 0.2553328 0.0695884 3.669187 0.0424185 0.0265846 0.0002433 0.5858290 0.9871982
chr18 79534269 0.9810294 0.7648669 0.2161625 0.0521380 4.145966 0.0415192 0.0271520 0.0000338 0.1737651 0.9870591
chr18 17696818 0.6270019 0.9085936 -0.2815917 0.0816511 -3.448717 0.0415192 0.0237971 0.0005633 0.9335171 0.9869271
chr18 19236470 0.6982535 0.8928256 -0.1945721 0.0425478 -4.573020 0.0415192 0.0265846 0.0000048 0.0489650 0.9868828
chr18 16283832 0.4708733 0.9776890 -0.5068157 0.1843811 -2.748740 0.0388707 0.0267905 0.0059825 0.9999991 0.9868205
chr18 83697832 0.8853226 0.5805762 0.3047464 0.0922442 3.303693 0.0317254 0.0211979 0.0009542 0.9999991 0.9867832
chr18 13258533 0.5591377 0.8502968 -0.2911591 0.0861916 -3.378044 0.0482875 0.0309170 0.0007300 0.9999991 0.9867199
chr18 67355238 0.9274049 0.7127643 0.2146406 0.0517357 4.148793 0.0415192 0.0265846 0.0000334 0.1734741 0.9866505
chr18 20133751 0.9898095 0.7171429 0.2726666 0.0780981 3.491334 0.0427333 0.0353624 0.0004806 0.8512054 0.9864793
chr18 10051980 0.7713326 0.5076365 0.2636961 0.0740853 3.559358 0.0294923 0.0263853 0.0003718 0.7609068 0.9864327
chr18 3210631 0.8595783 0.5412135 0.3183647 0.0988644 3.220217 0.0330071 0.0237560 0.0012809 0.9999991 0.9864149
chr18 86000834 0.9392838 0.6918537 0.2474302 0.0667408 3.707329 0.0358186 0.0294687 0.0002095 0.5386506 0.9864126
chr18 88652511 0.9598717 0.7039085 0.2559632 0.0706382 3.623582 0.0417470 0.0240065 0.0002906 0.6479708 0.9863752
chr18 37290275 0.4612712 0.7702699 -0.3089987 0.0947095 -3.262595 0.0288655 0.0216747 0.0011040 0.9999991 0.9863416
chr18 59172528 0.9407858 0.7414440 0.1993418 0.0450249 4.427372 0.0426999 0.0249688 0.0000095 0.0823512 0.9863212
chr18 52158629 0.4391881 0.6711874 -0.2319993 0.0598609 -3.875638 0.0415192 0.0265846 0.0001063 0.3546517 0.9862765
chr18 26499749 0.9004923 0.5984799 0.3020125 0.0916507 3.295256 0.0350715 0.0315042 0.0009833 0.9999991 0.9862491
chr18 9829220 0.7945722 0.4509168 0.3436554 0.1106013 3.107155 0.0552872 0.0294962 0.0018890 0.9999991 0.9862331
chr18 87855748 0.5515559 0.8385632 -0.2870073 0.0848708 -3.381698 0.0395813 0.0262333 0.0007204 0.9999991 0.9862206
chr18 89134558 0.9864468 0.7382886 0.2481582 0.0672614 3.689461 0.0421041 0.0193795 0.0002247 0.5573609 0.9861930
chr18 54822348 0.6018380 0.8681904 -0.2663524 0.0755956 -3.523385 0.0398200 0.0274181 0.0004261 0.8168850 0.9861169
chr18 27756748 0.9880580 0.7441493 0.2439087 0.0653984 3.729583 0.0426990 0.0197719 0.0001918 0.5063135 0.9861141
chr18 23367561 0.8276057 0.5447565 0.2828492 0.0831193 3.402931 0.0481572 0.0218279 0.0006667 0.9999991 0.9860930
chr18 41592049 0.8129749 0.4631494 0.3498255 0.1136381 3.078416 0.0313323 0.0228084 0.0020810 0.9999991 0.9860785
chr18 9617107 0.8484580 0.5729463 0.2755117 0.0799786 3.444819 0.0309170 0.0190695 0.0005714 0.9368586 0.9859010
chr18 48425946 0.9270399 0.6593883 0.2676516 0.0763970 3.503429 0.0349631 0.0263798 0.0004593 0.8348718 0.9859002
chr18 87020936 0.7207033 0.9506194 -0.2299161 0.0592022 -3.883573 0.0369330 0.0255697 0.0001029 0.3490797 0.9858983
chr18 62698278 0.5904027 0.9512146 -0.3608118 0.1189519 -3.033259 0.0346238 0.0269462 0.0024193 0.9999991 0.9858848
chr18 30722918 0.9857162 0.7003973 0.2853189 0.0845160 3.375917 0.0421082 0.0226469 0.0007357 0.9999991 0.9858384
chr18 18457110 0.7055889 0.9467469 -0.2411580 0.0644047 -3.744419 0.0455198 0.0219802 0.0001808 0.4846590 0.9858008
chr18 15470914 0.9495636 0.6790809 0.2704827 0.0778661 3.473689 0.0350087 0.0232819 0.0005134 0.8780332 0.9857183
chr18 48246940 0.7474738 0.9487325 -0.2012587 0.0463052 -4.346354 0.0481011 0.0277521 0.0000138 0.1026243 0.9856203
chr18 62698247 0.6348172 0.8323825 -0.1975653 0.0447173 -4.418097 0.0415192 0.0265846 0.0000100 0.0841151 0.9854388
chr18 30594587 0.6388002 0.8770981 -0.2382979 0.0634394 -3.756306 0.0430929 0.0265846 0.0001724 0.4703588 0.9853713
chr18 35601493 0.6436401 0.9784833 -0.3348432 0.1077860 -3.106555 0.0392889 0.0270516 0.0018928 0.9999991 0.9853538
chr18 54485297 0.9492661 0.7331881 0.2160780 0.0532731 4.056043 0.0425154 0.0335180 0.0000499 0.2235771 0.9853313
chr18 45307673 0.9634430 0.7236613 0.2397817 0.0641608 3.737198 0.0476530 0.0235486 0.0001861 0.4959256 0.9853199
chr18 86159732 0.9339732 0.6891281 0.2448451 0.0665281 3.680328 0.0367207 0.0233643 0.0002329 0.5676098 0.9852674
chr18 67579528 0.7784066 0.4998243 0.2785823 0.0820320 3.396020 0.0381621 0.0286816 0.0006837 0.9999991 0.9852610
chr18 49203335 0.9883950 0.7904826 0.1979124 0.0450064 4.397432 0.0423619 0.0323908 0.0000110 0.0892866 0.9852045
chr18 18477200 0.9779491 0.7904627 0.1874864 0.0402186 4.661678 0.0415754 0.0265846 0.0000031 0.0364304 0.9851950
chr18 27421715 0.4840842 0.7796012 -0.2955171 0.0899011 -3.287134 0.0401059 0.0225036 0.0010121 0.9999991 0.9851829
chr18 90069435 0.9818616 0.6670851 0.3147765 0.0987862 3.186442 0.0431797 0.0230708 0.0014403 0.9999991 0.9851667
chr18 63484643 0.5323635 0.8473621 -0.3149986 0.0991442 -3.177177 0.0420833 0.0260373 0.0014872 0.9999991 0.9849556
chr18 46514967 0.3844877 0.6593933 -0.2749056 0.0808153 -3.401654 0.0415192 0.0265846 0.0006698 0.9999991 0.9847797
chr18 86000984 0.9392838 0.6918537 0.2474302 0.0681566 3.630316 0.0347667 0.0374995 0.0002831 0.6426059 0.9847337
chr18 23183609 0.9771965 0.6598346 0.3173619 0.1006628 3.152722 0.0418743 0.0307189 0.0016176 0.9999991 0.9846037
chr18 17538082 0.9159539 0.7435078 0.1724461 0.0335728 5.136480 0.0390249 0.0265846 0.0000003 0.0057380 0.9845314
chr18 6363518 0.6757799 0.9165903 -0.2408104 0.0652855 -3.688572 0.0361910 0.0269111 0.0002255 0.5583188 0.9844910
chr18 11547092 0.3458383 0.6728578 -0.3270195 0.1052897 -3.105901 0.9894752 0.0469081 0.0018970 0.9999991 0.9844887
chr18 68462346 0.7566477 0.4697174 0.2869303 0.0867188 3.308744 0.0336976 0.0282709 0.0009372 0.9999991 0.9844463
chr18 27287605 0.9708749 0.6989293 0.2719456 0.0798166 3.407131 0.0453442 0.0244593 0.0006565 0.9999991 0.9843916
chr18 28617993 0.9852606 0.7143380 0.2709226 0.0793474 3.414386 0.0428104 0.0257977 0.0006393 0.9999991 0.9843855
chr18 67579523 0.7784066 0.4998243 0.2785823 0.0830582 3.354060 0.0392471 0.0286816 0.0007964 0.9999991 0.9842284
chr18 3500565 0.1414245 0.4056728 -0.2642483 0.0763957 -3.458944 0.0433442 0.9894752 0.0005423 0.9098710 0.9842221
chr18 71966060 0.9134439 0.5994790 0.3139649 0.0996956 3.149235 0.0458093 0.0391975 0.0016370 0.9999991 0.9840872
chr18 41352384 0.4928893 0.1652186 0.3276707 0.1060962 3.088430 0.0367389 0.0251211 0.0020122 0.9999991 0.9840869
chr18 54849908 0.7626734 0.3836918 0.3789816 0.1301598 2.911665 0.0381534 0.0262112 0.0035951 0.9999991 0.9840753
chr18 3999771 0.9749734 0.5588323 0.4161411 0.1478155 2.815273 0.0425018 0.0248129 0.0048736 0.9999991 0.9840121
chr18 43724810 0.6366228 0.3439624 0.2926604 0.0898892 3.255789 0.0320207 0.0213351 0.0011308 0.9999991 0.9839621
chr18 37149985 0.5403387 0.8969394 -0.3566007 0.1199721 -2.972365 0.0428778 0.0231094 0.0029552 0.9999991 0.9838462
chr18 85743044 0.9270750 0.7407774 0.1862976 0.0403294 4.619401 0.0415192 0.0265846 0.0000038 0.0422376 0.9838153
chr18 3308608 0.8046846 0.5129647 0.2917199 0.0897229 3.251344 0.0439124 0.0206777 0.0011486 0.9999991 0.9836992
chr18 66376599 0.9795930 0.7943525 0.1852405 0.0399163 4.640728 0.0415711 0.0265846 0.0000035 0.0393662 0.9836392
chr18 66376610 0.9795930 0.7943525 0.1852405 0.0399173 4.640606 0.0416344 0.0265846 0.0000035 0.0393662 0.9836369
chr18 30585066 0.4992208 0.7963285 -0.2971077 0.0923728 -3.216399 0.0363634 0.0267182 0.0012981 0.9999991 0.9835802
chr18 27287604 0.9708749 0.6989293 0.2719456 0.0806052 3.373797 0.0341056 0.0304307 0.0007414 0.9999991 0.9835471
chr18 19352203 0.8648601 0.5906464 0.2742137 0.0817061 3.356098 0.0390249 0.0236811 0.0007905 0.9999991 0.9835071
chr18 85814193 0.8936719 0.6879358 0.2057362 0.0495940 4.148411 0.0415192 0.0265846 0.0000335 0.1734741 0.9834981
chr18 50693565 0.7716809 0.5171528 0.2545281 0.0725086 3.510317 0.0337754 0.0268618 0.0004476 0.8288784 0.9834629
chr18 79694730 0.7339060 0.9341856 -0.2002795 0.0470808 -4.253949 0.0424810 0.0272733 0.0000210 0.1342867 0.9834119
chr18 84063168 0.7808151 0.5671723 0.2136428 0.0533712 4.002960 0.0415192 0.0265846 0.0000626 0.2564458 0.9833849
chr18 37467067 0.4834830 0.2160940 0.2673891 0.0786327 3.400482 0.0404029 0.0275880 0.0006727 0.9999991 0.9833639
chr18 14184063 0.9536770 0.6486621 0.3050149 0.0963251 3.166514 0.0326197 0.0216966 0.0015428 0.9999991 0.9833596
chr18 48357577 0.9454286 0.7342403 0.2111883 0.0522349 4.043051 0.0421147 0.0272364 0.0000528 0.2290934 0.9833572
chr18 83729630 0.7323883 0.9851920 -0.2528037 0.0719028 -3.515907 0.0314952 0.0271232 0.0004383 0.8252523 0.9832131
chr18 17884477 0.9462472 0.6513858 0.2948615 0.0917735 3.212928 0.0456207 0.0269953 0.0013139 0.9999991 0.9831436
chr18 87673321 0.9388216 0.6809874 0.2578342 0.0744048 3.465291 0.0447182 0.0257677 0.0005297 0.8974654 0.9830521
chr18 88694392 0.9820091 0.7423922 0.2396169 0.0658700 3.637725 0.0426215 0.0251991 0.0002751 0.6326491 0.9829795
chr18 74100821 0.8773801 0.6275973 0.2497828 0.0707058 3.532705 0.0429205 0.0264586 0.0004113 0.8120801 0.9829295
chr18 70098717 0.9882065 0.7825056 0.2057008 0.0499410 4.118878 0.0420335 0.0219478 0.0000381 0.1855471 0.9828495
chr18 24126030 0.4007034 0.6277292 -0.2270257 0.0600523 -3.780467 0.0415192 0.0265846 0.0001565 0.4402395 0.9827958
chr18 77640304 0.9826323 0.7808425 0.2017899 0.0481536 4.190548 0.0415192 0.0265846 0.0000278 0.1565509 0.9827364
chr18 26475032 0.8924472 0.6417235 0.2507237 0.0713192 3.515517 0.0386940 0.0205635 0.0004389 0.8252523 0.9827158
chr18 48446248 0.2555459 0.5246844 -0.2691385 0.0801859 -3.356433 0.0738805 0.0216130 0.0007895 0.9999991 0.9825440
chr18 19943680 0.8462134 0.5662033 0.2800102 0.0854317 3.277593 0.0435541 0.0201306 0.0010470 0.9999991 0.9824484
chr18 41030023 0.9260253 0.6760239 0.2500014 0.0712807 3.507281 0.0290628 0.0213829 0.0004527 0.8313663 0.9823276
chr18 87218173 0.9351370 0.6415444 0.2935926 0.0920762 3.188581 0.0399772 0.0251488 0.0014297 0.9999991 0.9822559
chr18 55441667 0.7136627 0.9523101 -0.2386474 0.0659451 -3.618879 0.0620741 0.0282658 0.0002959 0.6556634 0.9822439
chr18 22627105 0.7133156 0.9799193 -0.2666037 0.0792881 -3.362469 0.0494814 0.0269319 0.0007725 0.9999991 0.9821922
chr18 45861435 0.5050306 0.2538460 0.2511846 0.0720479 3.486356 0.0401165 0.0264994 0.0004896 0.8584803 0.9820652
chr18 68366602 0.6803562 0.9177724 -0.2374163 0.0655037 -3.624470 0.0414346 0.0265846 0.0002896 0.6475676 0.9820404
chr18 11159220 0.8686023 0.6185800 0.2500223 0.0716645 3.488790 0.0375896 0.0297978 0.0004852 0.8560870 0.9818437
chr18 60014130 0.8940994 0.6599910 0.2341085 0.0640758 3.653618 0.0415192 0.0265846 0.0002586 0.6098240 0.9818240
chr18 71926814 0.7059018 0.9082308 -0.2023290 0.0488974 -4.137824 0.0415192 0.0265846 0.0000351 0.1770655 0.9818132
chr18 27171646 0.8680764 0.6136796 0.2543969 0.0738045 3.446900 0.0604160 0.9894752 0.0005671 0.9367906 0.9817802
chr18 18389147 0.8265674 0.4999322 0.3266352 0.1084443 3.012008 0.0376572 0.0290654 0.0025953 0.9999991 0.9817273
chr18 50642246 0.8586850 0.6079151 0.2507699 0.0721671 3.474853 0.0398992 0.0273634 0.0005111 0.8780332 0.9816548
chr18 43888895 0.6876475 0.9267737 -0.2391262 0.0666475 -3.587927 0.0330645 0.0274649 0.0003333 0.7039263 0.9815784
chr18 28276824 0.8764927 0.5963819 0.2801108 0.0863638 3.243381 0.0415192 0.0265846 0.0011812 0.9999991 0.9814929
chr18 6745842 0.8882682 0.4724788 0.4157894 0.1523415 2.729325 0.0376178 0.0214707 0.0063464 0.9999991 0.9812644
chr18 13656602 0.8781703 0.6299638 0.2482066 0.0712589 3.483165 0.0393188 0.0218167 0.0004955 0.8622718 0.9812300
chr18 52859438 0.9121148 0.5450528 0.3670621 0.1286674 2.852798 0.0343987 0.0239086 0.0043336 0.9999991 0.9811762
chr18 16327907 0.7921129 0.5290478 0.2630651 0.0785334 3.349722 0.0415192 0.0265846 0.0008089 0.9999991 0.9810724
chr18 81156264 0.9256361 0.6760925 0.2495436 0.0720675 3.462636 0.0367250 0.0265125 0.0005349 0.9026388 0.9810096
chr18 74100718 0.8773801 0.6275973 0.2497828 0.0722153 3.458863 0.0478249 0.0300196 0.0005425 0.9098710 0.9809663
chr18 10584146 0.7635770 0.9877138 -0.2241368 0.0598981 -3.741966 0.0380782 0.0278024 0.0001826 0.4884748 0.9808890
chr18 29436419 0.6783752 0.4106323 0.2677429 0.0809573 3.307211 0.0557490 0.0255387 0.0009423 0.9999991 0.9808697
chr18 71488060 0.9263774 0.7384891 0.1878884 0.0424194 4.429304 0.0415192 0.0265846 0.0000095 0.0823512 0.9808622
chr18 41819190 0.7334878 0.4230172 0.3104705 0.1017250 3.052056 0.0297207 0.0233395 0.0022728 0.9999991 0.9807549
chr18 7052460 0.8678145 0.6247400 0.2430745 0.0692011 3.512582 0.0415192 0.0298622 0.0004438 0.8272376 0.9806577
chr18 33764291 0.9474019 0.7484057 0.1989963 0.0478864 4.155587 0.0415192 0.0265846 0.0000324 0.1706553 0.9806477
chr18 10584147 0.7635770 0.9877138 -0.2241368 0.0600895 -3.730048 0.0311486 0.0268773 0.0001914 0.5063135 0.9805794
chr18 37291195 0.6756089 0.9392182 -0.2636092 0.0792474 -3.326407 0.0414240 0.0275617 0.0008797 0.9999991 0.9805188
chr18 54427637 0.9886254 0.7948597 0.1937657 0.0454251 4.265612 0.0423302 0.0251396 0.0000199 0.1292413 0.9804999
chr18 31248396 0.3675608 0.7427996 -0.3752388 0.1335997 -2.808679 0.0374946 0.0223513 0.0049745 0.9999991 0.9804965
chr18 11547091 0.3458383 0.6728578 -0.3270195 0.1101953 -2.967636 0.9894752 0.0675439 0.0030010 0.9999991 0.9803615
chr18 83609827 0.6110777 0.8826321 -0.2715545 0.0834258 -3.255041 0.0450246 0.0300861 0.0011338 0.9999991 0.9801309
chr18 62858778 0.9817661 0.7251615 0.2566046 0.0761650 3.369062 0.0418129 0.0191127 0.0007542 0.9999991 0.9801161 


# call differentially methylated regions
dmrs <- callDMR(dmlTest, delta=0.1, p.threshold=0.01)
# write DMR results to file
write.table(dmrs, file="Differential_methylation_regions_24Mvs3M.txt", sep="\t", col.names=T, row.names=F, quote=F)
# list DMRs
n <- ncol(dmrs)
header1 <- n
names(header1) <- paste0("Number of differentially methylated regions = ", nrow(dmrs))
header2 <- n
names(header2) <- "The list of DMRs:"
kable(dmrs, align = 'c', row.names=F) %>%
  add_header_above(header1, align = 'l') %>%
  add_header_above(header2, font_size = "larger", bold = T, align = "l") %>%
  kable_styling(bootstrap_options = c("hover", "condensed", "responsive"), full_width = T) %>%
  scroll_box(height = "500px")
The list of DMRs:
Number of differentially methylated regions = 1
chr start end length nCG meanMethy1 meanMethy2 diff.Methy areaStat
chr18 10051981 10052246 266 43 0.702096 0.4445933 0.2575028 174.9704
Visualization of individual DMR


showOneDMR(dmrs[1,], BSobj)


R session information

sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.7 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] DSS_2.36.0                  bsseq_1.24.4               
 [7] SummarizedExperiment_1.18.2 DelayedArray_0.14.1        
 [9] matrixStats_0.56.0          GenomicRanges_1.40.0       
[11] GenomeInfoDb_1.24.2         IRanges_2.22.2             
[13] S4Vectors_0.26.1            BiocParallel_1.22.0        
[15] Biobase_2.48.0              BiocGenerics_0.34.0        
[17] 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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