SIMD 1.2.0
This package provides a inferential analysis method for detecting differentially expressed CpG sites in MeDIP-seq data. It uses statistical framework and EM algorithm, to identify differentially expressed CpG sites. The methods on this package are described in the article Methylation-level Inferences and Detection of Differential Methylation with Medip-seq Data by Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang and Xiyan Yang (2018, pending publication).
SIMD method is developed for jointly analyzing MeDIP-seq and MRE-seq data, which are derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq) and methyl-sensitive restriction enzymes experiments for unmethylated CpGs (MRE-seq). We have implemented the SIMD method via a set of R functions with the computational intensive parts written in C. We make a R package named SIMD, which is the abbreviation of Statistical Inferences with MeDIP-seq Data, and give a tutorial for the package. The method consist three steps.
Step 1: Data Pre-processing;
Step 2: Calculating p-values of each CpG site by the EM algorithm;
Step 3: Select Significants.
We use a part of a real dataset to illustrate the usage of the SIMD package. The programs can run under the Linux system and windows 10 system. The R versions should larger than 3.5.0.
Before installing SIMD package, the user must install three other R pack- ages, which can be done using the following commands:
install.packages("BiocManager")
BiocManager::install(c('edgeR', 'statmod','methylMnM'))
library(edgeR)
library(statmod)
library(methylMnM)Next, to install the SIMD package into your R environment, start R and enter:
BiocManager::install("SIMD")Then, the SIMD package is ready to load.
library(SIMD)In order to reproduce the presented SIMD workflow, the package includes the example data sets, which is a part of a real data sets, including:
all_CpGsite_bin_chr18,
three_mre_cpg,
EM2_H1ESB1_MeDIP_sigleCpG,
EM2_H1ESB2_MeDIP_sigleCpG,
H1ESB1_MRE_sigleCpG,
and H1ESB2_MRE_sigleCpG, which is included in file example_data.RDdata in
the data subdirectory of the SIMD package.
The files contain genomic regions from chromosome 18 only, as covered by short reads obtained from a MeDIP and MRE experiment of human H1ESB1 cells.
All output files are in a .bed format. The input file contain the following columns.
For MRE-seq data, we need “+” and “-” strand information in mapping process, which is general located at the sixth column of the input file. Each row represents a mapped read. These information can be extracted from the output file(s) of common mapping tools.
The SIMD program requires users to provide the genome-wide MeDIP-seq and MRE-seq reads and the reference genome. The pre-processing step involves calculation of MeDIP-seq and MRE-seq count and CpG and MRE-specific count in each CpG site. The mainly steps please refer the data pre-processing steps of R package MethylMnM.
In this manual, we use example data located in the data subdirectory of the SIMD package, and the example data is processed by MethylMnM package in advance. The path is:
datafile <- system.file("extdata", package="methylMnM")
filepath <- datafile[1]The CpG count, MRE-CpG count, MeDIP-seq count and MRE-seq count of each site are stored at:
dirwrite <- paste(setwd(getwd()), "/", sep="")Then we compute the number of actual short reads in each CpG site by the function of EMalgorithm(), which use EM algorithm to infer the actual reads by the observation fragments. The results are saved in file writefile and reportfile. We give an example as follows, the data is from data subdirectory of the SIMD package:
data(example_data)
allcpgfile <- EM_H1ESB1_MeDIP_sigleCpG
readshort <- paste(filepath, "/H1ESB1_MeDIP_18.extended.txt", sep="")
writefile <- paste(dirwrite, "EM2_H1ESB1_MeDIP_sigleCpG.bed", sep="")
reportfile <- paste(dirwrite, "EM2_H1ESB1_MeDIP_sigleCpG_report.bed", sep="")
EMalgorithm(cpgsitefile=readshort, allcpgfile=allcpgfile, category="1",
writefile=writefile, reportfile=reportfile)## [1] 1## V1 V2 V3 V4
## 1 chr18 10692 10694 2.699262074
## 2 chr18 10703 10705 3.464033797
## 3 chr18 10718 10720 5.013880075
## 4 chr18 10730 10732 4.575160390
## 5 chr18 10753 10755 4.367140836
## 6 chr18 10767 10769 3.949686891
## 7 chr18 10787 10789 3.006196402
## 8 chr18 10791 10793 2.721496577
## 9 chr18 10795 10797 2.703602326
## 10 chr18 10815 10817 2.514884741
## 11 chr18 10823 10825 2.335973283
## 12 chr18 10829 10831 2.380368655
## 13 chr18 10831 10833 2.380368655
## 14 chr18 10839 10841 2.226858406
## 15 chr18 10861 10863 1.500303502
## 16 chr18 10869 10871 1.248835637
## 17 chr18 10875 10877 1.136110056
## 18 chr18 10887 10889 0.831184543
## 19 chr18 10921 10923 0.232070026
## 20 chr18 10929 10931 0.232070026
## 21 chr18 10934 10936 0.232070026
## 22 chr18 10937 10939 0.232070026
## 23 chr18 10940 10942 0.179499689
## 24 chr18 10946 10948 0.131977440
## 25 chr18 10948 10950 0.090078076
## 26 chr18 10956 10958 0.090078076
## 27 chr18 10958 10960 0.090078076
## 28 chr18 10963 10965 0.090078076
## 29 chr18 10966 10968 0.056609652
## 30 chr18 10969 10971 0.056609652
## 31 chr18 10975 10977 0.028689994
## 32 chr18 10977 10979 0.028689994
## 33 chr18 10985 10987 0.028689994
## 34 chr18 10987 10989 0.028689994
## 35 chr18 10992 10994 0.028689994
## 36 chr18 10995 10997 0.028689994
## 37 chr18 10998 11000 0.028689994
## 38 chr18 11004 11006 0.007633588
## 39 chr18 11006 11008 0.007633588
## 40 chr18 11014 11016 0.007633588
## 41 chr18 11016 11018 0.007633588
## 42 chr18 11021 11023 0.000000000
## 43 chr18 11024 11026 0.000000000
## 44 chr18 11027 11029 0.000000000
## 45 chr18 11033 11035 0.000000000
## 46 chr18 11035 11037 0.000000000
## 47 chr18 11043 11045 0.000000000
## 48 chr18 11045 11047 0.000000000
## 49 chr18 11050 11052 0.000000000
## 50 chr18 11053 11055 0.000000000
## 51 chr18 11056 11058 0.000000000
## 52 chr18 11062 11064 0.000000000
## 53 chr18 11064 11066 0.000000000
## 54 chr18 11072 11074 0.000000000
## 55 chr18 11074 11076 0.000000000
## 56 chr18 11079 11081 0.000000000
## 57 chr18 11082 11084 0.000000000
## 58 chr18 11085 11087 0.000000000
## 59 chr18 11091 11093 0.000000000
## 60 chr18 11097 11099 0.000000000
## 61 chr18 11099 11101 0.000000000
## 62 chr18 11107 11109 0.000000000
## 63 chr18 11109 11111 0.000000000
## 64 chr18 11114 11116 0.000000000
## 65 chr18 11117 11119 0.000000000
## 66 chr18 11120 11122 0.000000000
## 67 chr18 11126 11128 0.012987013
## 68 chr18 11132 11134 0.052289815
## 69 chr18 11134 11136 0.052289815
## 70 chr18 11142 11144 0.215690742
## 71 chr18 11144 11146 0.215690742
## 72 chr18 11148 11150 0.215690742
## 73 chr18 11154 11156 0.215690742
## 74 chr18 11167 11169 0.752458799
## 75 chr18 11218 11220 1.778161361
## 76 chr18 11230 11232 2.067471968
## 77 chr18 11251 11253 2.381065646
## 78 chr18 11256 11258 2.381065646
## 79 chr18 11323 11325 1.586947232
## 80 chr18 11325 11327 1.586947232
## 81 chr18 11344 11346 1.304016697
## 82 chr18 11354 11356 1.304016697
## 83 chr18 11358 11360 1.080206567
## 84 chr18 11386 11388 1.357217972
## 85 chr18 11400 11402 1.498522320
## 86 chr18 11405 11407 1.498522320
## 87 chr18 11431 11433 1.934716599
## 88 chr18 11511 11513 1.633333333
## 89 chr18 11532 11534 1.250000000
## 90 chr18 11611 11613 1.254824561
## 91 chr18 11667 11669 0.583859649
## 92 chr18 11708 11710 0.583859649
## 93 chr18 11723 11725 1.006224256
## 94 chr18 11739 11741 0.753592677
## 95 chr18 11753 11755 0.427993898
## 96 chr18 11755 11757 0.306372276
## 97 chr18 11761 11763 0.306372276
## 98 chr18 11783 11785 0.306372276
## 99 chr18 11791 11793 0.306372276
## 100 chr18 11793 11795 0.306372276
## 101 chr18 11805 11807 0.165097821
## 102 chr18 11823 11825 0.165097821
## 103 chr18 11825 11827 0.165097821
## 104 chr18 11831 11833 0.240156060
## 105 chr18 11838 11840 0.330145314
## 106 chr18 11849 11851 0.643594231
## 107 chr18 11852 11854 0.643594231
## 108 chr18 11854 11856 0.643594231
## 109 chr18 11863 11865 0.544895607
## 110 chr18 11888 11890 0.498807414
## 111 chr18 11891 11893 0.498807414
## 112 chr18 11893 11895 0.498807414
## 113 chr18 11911 11913 0.465345380
## 114 chr18 11914 11916 0.465345380
## 115 chr18 11939 11941 1.006700023
## 116 chr18 11947 11949 1.006700023
## 117 chr18 11955 11957 1.006700023
## 118 chr18 11962 11964 1.006700023
## 119 chr18 11988 11990 1.328539266
## 120 chr18 11990 11992 1.328539266
## 121 chr18 11996 11998 1.297397153
## 122 chr18 12009 12011 1.260655285
## 123 chr18 12011 12013 1.096611451
## 124 chr18 12022 12024 0.938165718
## 125 chr18 12033 12035 1.079141471
## 126 chr18 12049 12051 1.069957085
## 127 chr18 12052 12054 1.069957085
## 128 chr18 12058 12060 1.069957085
## 129 chr18 12064 12066 1.232874600
## 130 chr18 12067 12069 0.960711886
## 131 chr18 12077 12079 1.014600378
## 132 chr18 12087 12089 0.894328774
## 133 chr18 12101 12103 0.894328774
## 134 chr18 12116 12118 0.799992328
## 135 chr18 12122 12124 0.690645692
## 136 chr18 12139 12141 0.499492449
## 137 chr18 12142 12144 0.499492449
## 138 chr18 12153 12155 0.332982687
## 139 chr18 12160 12162 0.667655848
## 140 chr18 12179 12181 0.635949061
## 141 chr18 12181 12183 0.635949061
## 142 chr18 12204 12206 0.714002799
## 143 chr18 12210 12212 0.768703286
## 144 chr18 12216 12218 0.768703286
## 145 chr18 12223 12225 0.520160207
## 146 chr18 12249 12251 1.649798014
## 147 chr18 12257 12259 1.569077544
## 148 chr18 12272 12274 1.841020424
## 149 chr18 12278 12280 2.145278803
## 150 chr18 12280 12282 2.145278803
## 151 chr18 12293 12295 2.684583553
## 152 chr18 12297 12299 2.881336107
## 153 chr18 12312 12314 2.708051515
## 154 chr18 12336 12338 3.231561757
## 155 chr18 12347 12349 3.557225147
## 156 chr18 12350 12352 3.843967217
## 157 chr18 12361 12363 4.021983139
## 158 chr18 12370 12372 4.738570382
## 159 chr18 12397 12399 4.053435423
## 160 chr18 12436 12438 4.464875891
## 161 chr18 12485 12487 4.155906381
## 162 chr18 12506 12508 4.485778804
## 163 chr18 12527 12529 5.386038747
## 164 chr18 12554 12556 4.969034214
## 165 chr18 12560 12562 4.603399740
## 166 chr18 12570 12572 4.417559580
## 167 chr18 12584 12586 5.875979779
## 168 chr18 12633 12635 6.706979747
## 169 chr18 12709 12711 4.963922243
## 170 chr18 12779 12781 1.448412698
## 171 chr18 12794 12796 0.535714286
## 172 chr18 12855 12857 0.581818182
## 173 chr18 12904 12906 2.254761905
## 174 chr18 12907 12909 2.726406926
## 175 chr18 12953 12955 6.237132651
## 176 chr18 12968 12970 5.809636434
## 177 chr18 13092 13094 3.305587818
## 178 chr18 13118 13120 2.056507937
## 179 chr18 13232 13234 3.563581795
## 180 chr18 13245 13247 3.370989202
## 181 chr18 13262 13264 7.480023511
## 182 chr18 13334 13336 5.346886973
## 183 chr18 13412 13414 4.600000000
## 184 chr18 13548 13550 0.000000000
## 185 chr18 13582 13584 0.000000000
## 186 chr18 13703 13705 0.000000000
## 187 chr18 13866 13868 7.000000000
## 188 chr18 13993 13995 7.500000000
## 189 chr18 14004 14006 7.500000000
## 190 chr18 14235 14237 0.000000000
## 191 chr18 14438 14440 0.000000000
## 192 chr18 14502 14504 0.000000000
## 193 chr18 14522 14524 0.000000000
## 194 chr18 14553 14555 0.000000000
## 195 chr18 14555 14557 0.000000000
## 196 chr18 14576 14578 0.000000000
## 197 chr18 14745 14747 0.000000000
## 198 chr18 14813 14815 0.000000000
## 199 chr18 14839 14841 0.000000000
## 200 chr18 14891 14893 0.000000000
## 201 chr18 15470 15472 0.000000000
## 202 chr18 16066 16068 0.000000000
## 203 chr18 16587 16589 0.000000000
## 204 chr18 17144 17146 0.000000000
## 205 chr18 17914 17916 0.000000000
## 206 chr18 17999 18001 0.000000000
## 207 chr18 18097 18099 0.000000000
## 208 chr18 18113 18115 0.000000000
## 209 chr18 18396 18398 0.000000000
## 210 chr18 18465 18467 0.000000000
## 211 chr18 18543 18545 0.000000000
## 212 chr18 19188 19190 0.000000000
## 213 chr18 19414 19416 0.000000000
## 214 chr18 19944 19946 0.000000000
## 215 chr18 20001 20003 0.000000000
## 216 chr18 20063 20065 0.000000000
## 217 chr18 20095 20097 0.000000000
## 218 chr18 20179 20181 0.000000000
## 219 chr18 20182 20184 0.000000000
## 220 chr18 20685 20687 1.000000000
## 221 chr18 20872 20874 0.000000000
## 222 chr18 21235 21237 0.000000000
## 223 chr18 21329 21331 0.000000000
## 224 chr18 21659 21661 0.000000000
## 225 chr18 21683 21685 0.000000000
## 226 chr18 21705 21707 0.000000000
## 227 chr18 21739 21741 0.000000000
## 228 chr18 21769 21771 0.000000000
## 229 chr18 21778 21780 0.000000000
## 230 chr18 21861 21863 0.000000000
## 231 chr18 21988 21990 0.000000000
## 232 chr18 22336 22338 0.000000000
## 233 chr18 22841 22843 0.000000000
## 234 chr18 23029 23031 0.000000000
## 235 chr18 23066 23068 0.000000000
## 236 chr18 23281 23283 0.000000000
## 237 chr18 23401 23403 0.000000000
## 238 chr18 23439 23441 0.000000000
## 239 chr18 23456 23458 0.000000000
## 240 chr18 23476 23478 0.000000000
## 241 chr18 23515 23517 0.000000000
## 242 chr18 23557 23559 0.000000000
## 243 chr18 23851 23853 0.000000000
## 244 chr18 23927 23929 0.000000000
## 245 chr18 24575 24577 0.000000000
## 246 chr18 25082 25084 0.000000000
## 247 chr18 25270 25272 0.000000000
## 248 chr18 25286 25288 0.000000000
## 249 chr18 25421 25423 0.000000000
## 250 chr18 25660 25662 0.000000000
## 251 chr18 25865 25867 0.000000000
## 252 chr18 25871 25873 0.000000000
## 253 chr18 26060 26062 0.000000000
## 254 chr18 26187 26189 0.000000000
## 255 chr18 26196 26198 0.000000000
## 256 chr18 26327 26329 0.000000000
## 257 chr18 26627 26629 0.200000000
## 258 chr18 26661 26663 0.733333333
## 259 chr18 26690 26692 0.733333333
## 260 chr18 26713 26715 0.166666667
## 261 chr18 26792 26794 0.166666667
## 262 chr18 26802 26804 0.000000000
## 263 chr18 26807 26809 0.000000000
## 264 chr18 26845 26847 0.000000000
## 265 chr18 26847 26849 0.000000000
## 266 chr18 26858 26860 0.000000000
## 267 chr18 26944 26946 0.000000000
## 268 chr18 26988 26990 0.000000000
## 269 chr18 27167 27169 0.000000000
## 270 chr18 27208 27210 0.000000000
## 271 chr18 27819 27821 0.344720497
## 272 chr18 27828 27830 0.344720497
## 273 chr18 27847 27849 0.919772257
## 274 chr18 27915 27917 1.343726708
## 275 chr18 27929 27931 1.343726708
## 276 chr18 27947 27949 0.902380952
## 277 chr18 27970 27972 0.327142857
## 278 chr18 27982 27984 0.327142857
## 279 chr18 27992 27994 0.146666667
## 280 chr18 28007 28009 0.000000000
## 281 chr18 28022 28024 0.000000000
## 282 chr18 28032 28034 0.000000000
## 283 chr18 28040 28042 0.000000000
## 284 chr18 28053 28055 0.000000000
## 285 chr18 28142 28144 0.000000000
## 286 chr18 28151 28153 0.000000000
## 287 chr18 28171 28173 0.000000000
## 288 chr18 28204 28206 0.000000000
## 289 chr18 28221 28223 0.000000000
## 290 chr18 28234 28236 0.000000000
## 291 chr18 28368 28370 0.000000000
## 292 chr18 28379 28381 0.000000000
## 293 chr18 28387 28389 0.000000000
## 294 chr18 28426 28428 0.000000000
## 295 chr18 28495 28497 0.000000000
## 296 chr18 28501 28503 0.000000000
## 297 chr18 28524 28526 0.000000000
## 298 chr18 28544 28546 0.000000000
## 299 chr18 28562 28564 0.000000000
## 300 chr18 28666 28668 0.000000000
## 301 chr18 28733 28735 0.000000000
## 302 chr18 28833 28835 0.000000000
## 303 chr18 28853 28855 0.000000000
## 304 chr18 28895 28897 0.000000000
## 305 chr18 28912 28914 0.000000000
## 306 chr18 29146 29148 0.000000000
## 307 chr18 29221 29223 0.000000000
## 308 chr18 29422 29424 0.000000000
## 309 chr18 29431 29433 0.000000000
## 310 chr18 29652 29654 0.000000000
## 311 chr18 29918 29920 0.000000000
## 312 chr18 29976 29978 0.000000000
## 313 chr18 30288 30290 0.000000000
## 314 chr18 30385 30387 0.000000000
## 315 chr18 30591 30593 0.000000000
## 316 chr18 30870 30872 0.000000000
## 317 chr18 30893 30895 0.000000000
## 318 chr18 30936 30938 0.000000000
## 319 chr18 31098 31100 0.000000000
## 320 chr18 31461 31463 0.000000000
## 321 chr18 31914 31916 0.000000000
## 322 chr18 31930 31932 0.000000000
## 323 chr18 32210 32212 0.000000000
## 324 chr18 32477 32479 0.000000000
## 325 chr18 32732 32734 0.000000000
## 326 chr18 32824 32826 0.000000000
## 327 chr18 33717 33719 0.000000000
## 328 chr18 34235 34237 0.000000000
## 329 chr18 34281 34283 0.000000000
## 330 chr18 34319 34321 0.000000000
## 331 chr18 34334 34336 0.000000000
## 332 chr18 34857 34859 0.000000000
## 333 chr18 34972 34974 0.000000000
## 334 chr18 34976 34978 0.000000000
## 335 chr18 35523 35525 0.000000000
## 336 chr18 35845 35847 0.000000000
## 337 chr18 35851 35853 0.000000000
## 338 chr18 35863 35865 0.000000000
## 339 chr18 35929 35931 0.000000000
## 340 chr18 35947 35949 0.000000000
## 341 chr18 35952 35954 0.000000000
## 342 chr18 35963 35965 0.000000000
## 343 chr18 35990 35992 0.000000000
## 344 chr18 35997 35999 0.000000000
## 345 chr18 36062 36064 0.206349206
## 346 chr18 36077 36079 0.206349206
## 347 chr18 36097 36099 0.206349206
## 348 chr18 36111 36113 0.732698413
## 349 chr18 36114 36116 0.732698413
## 350 chr18 36153 36155 0.732698413
## 351 chr18 36157 36159 0.382857143
## 352 chr18 36171 36173 0.160000000
## 353 chr18 36178 36180 0.160000000
## 354 chr18 36190 36192 0.160000000
## 355 chr18 36218 36220 0.160000000
## 356 chr18 36239 36241 0.160000000
## 357 chr18 36285 36287 0.000000000
## 358 chr18 36425 36427 0.000000000
## 359 chr18 36557 36559 0.000000000
## 360 chr18 36660 36662 0.000000000
## 361 chr18 36697 36699 0.000000000
## 362 chr18 36743 36745 0.000000000
## 363 chr18 36840 36842 0.000000000
## 364 chr18 36861 36863 0.000000000
## 365 chr18 36987 36989 0.000000000
## 366 chr18 36996 36998 0.000000000
## 367 chr18 37023 37025 0.000000000
## 368 chr18 37028 37030 0.000000000
## 369 chr18 37054 37056 0.000000000
## 370 chr18 37083 37085 0.000000000
## 371 chr18 37170 37172 0.000000000
## 372 chr18 37321 37323 0.000000000
## 373 chr18 37410 37412 0.000000000
## 374 chr18 37677 37679 0.000000000
## 375 chr18 37720 37722 0.000000000
## 376 chr18 37749 37751 0.000000000
## 377 chr18 37915 37917 0.000000000
## 378 chr18 38642 38644 0.000000000
## 379 chr18 38982 38984 0.000000000
## 380 chr18 39033 39035 0.000000000
## 381 chr18 39210 39212 0.000000000
## 382 chr18 39521 39523 0.000000000
## 383 chr18 39801 39803 0.000000000
## 384 chr18 39887 39889 0.000000000
## 385 chr18 40212 40214 0.000000000
## 386 chr18 40339 40341 0.000000000
## 387 chr18 40502 40504 0.000000000
## 388 chr18 40680 40682 0.000000000
## 389 chr18 41251 41253 0.000000000
## 390 chr18 41359 41361 0.000000000
## 391 chr18 41372 41374 0.000000000
## 392 chr18 41407 41409 0.000000000
## 393 chr18 41552 41554 0.000000000
## 394 chr18 41575 41577 0.000000000
## 395 chr18 41740 41742 0.000000000
## 396 chr18 41953 41955 0.000000000
## 397 chr18 42652 42654 0.000000000
## 398 chr18 42831 42833 0.000000000
## 399 chr18 43156 43158 0.000000000
## 400 chr18 43562 43564 0.000000000
## 401 chr18 43610 43612 0.000000000
## 402 chr18 43619 43621 0.000000000
## 403 chr18 43640 43642 0.000000000
## 404 chr18 43704 43706 1.000000000
## 405 chr18 44032 44034 0.000000000
## 406 chr18 44211 44213 0.000000000
## 407 chr18 44548 44550 0.000000000
## 408 chr18 44589 44591 0.000000000
## 409 chr18 44611 44613 0.000000000
## 410 chr18 44795 44797 0.000000000
## 411 chr18 44798 44800 0.000000000
## 412 chr18 44811 44813 0.000000000
## 413 chr18 45139 45141 0.000000000
## 414 chr18 45322 45324 0.000000000
## 415 chr18 45425 45427 0.000000000
## 416 chr18 45676 45678 1.000000000
## 417 chr18 45678 45680 1.000000000
## 418 chr18 45750 45752 0.000000000
## 419 chr18 45867 45869 0.000000000
## 420 chr18 45950 45952 0.000000000
## 421 chr18 46049 46051 0.333333333
## 422 chr18 46140 46142 0.333333333
## 423 chr18 46191 46193 0.333333333
## 424 chr18 46232 46234 0.500000000
## 425 chr18 46240 46242 0.500000000
## 426 chr18 46627 46629 1.666666667
## 427 chr18 46655 46657 0.333333333
## 428 chr18 46797 46799 0.000000000
## 429 chr18 46928 46930 0.000000000
## 430 chr18 47085 47087 1.000000000
## 431 chr18 47147 47149 0.000000000
## 432 chr18 47167 47169 0.000000000
## 433 chr18 47253 47255 0.000000000
## 434 chr18 47278 47280 0.000000000
## 435 chr18 47312 47314 0.000000000
## 436 chr18 47406 47408 0.000000000
## 437 chr18 47433 47435 0.000000000
## 438 chr18 47437 47439 0.000000000
## 439 chr18 47475 47477 0.000000000
## 440 chr18 47490 47492 0.000000000
## 441 chr18 47496 47498 0.000000000
## 442 chr18 47523 47525 0.200000000
## 443 chr18 47527 47529 0.200000000
## 444 chr18 47552 47554 0.200000000
## 445 chr18 47608 47610 0.200000000
## 446 chr18 47648 47650 0.200000000
## 447 chr18 47667 47669 0.142857143
## 448 chr18 47679 47681 0.142857143
## 449 chr18 47685 47687 0.142857143
## 450 chr18 47765 47767 0.142857143
## 451 chr18 47788 47790 0.142857143
## 452 chr18 47802 47804 0.142857143
## 453 chr18 47807 47809 0.142857143
## 454 chr18 47879 47881 0.000000000
## 455 chr18 47897 47899 0.000000000
## 456 chr18 47919 47921 0.000000000
## 457 chr18 47939 47941 0.000000000
## 458 chr18 47947 47949 0.000000000
## 459 chr18 47961 47963 0.000000000
## 460 chr18 47972 47974 0.000000000
## 461 chr18 48002 48004 0.000000000
## 462 chr18 48106 48108 0.250000000
## 463 chr18 48111 48113 0.250000000
## 464 chr18 48136 48138 0.250000000
## 465 chr18 48138 48140 0.250000000
## 466 chr18 48171 48173 0.250000000
## 467 chr18 48189 48191 0.250000000
## 468 chr18 48196 48198 0.250000000
## 469 chr18 48208 48210 0.250000000
## 470 chr18 48257 48259 0.000000000
## 471 chr18 48369 48371 0.000000000
## 472 chr18 48385 48387 0.000000000
## 473 chr18 48394 48396 0.000000000
## 474 chr18 48396 48398 0.000000000
## 475 chr18 48410 48412 0.000000000
## 476 chr18 48432 48434 0.000000000
## 477 chr18 48464 48466 1.000000000
## 478 chr18 48472 48474 1.000000000
## 479 chr18 48475 48477 1.000000000
## 480 chr18 48487 48489 1.000000000
## 481 chr18 48555 48557 1.000000000
## 482 chr18 48649 48651 0.000000000
## 483 chr18 48664 48666 0.000000000
## 484 chr18 48708 48710 0.254257492
## 485 chr18 48726 48728 0.762748231
## 486 chr18 48765 48767 1.578811665
## 487 chr18 48779 48781 1.837513618
## 488 chr18 48806 48808 2.744871979
## 489 chr18 48811 48813 2.744871979
## 490 chr18 48816 48818 2.768205312
## 491 chr18 48819 48821 2.431456662
## 492 chr18 48847 48849 2.386328227
## 493 chr18 48911 48913 0.482177486
## 494 chr18 48925 48927 0.352794964
## 495 chr18 48929 48931 0.352794964
## 496 chr18 48939 48941 0.435897436
## 497 chr18 48972 48974 0.168929110
## 498 chr18 48982 48984 0.168929110
## 499 chr18 49006 49008 0.058823529
## 500 chr18 49020 49022 0.058823529
## 501 chr18 49029 49031 0.058823529
## 502 chr18 49031 49033 0.058823529
## 503 chr18 49038 49040 0.058823529
## 504 chr18 49053 49055 0.058823529
## 505 chr18 49060 49062 0.058823529
## 506 chr18 49074 49076 0.058823529
## 507 chr18 49086 49088 0.058823529
## 508 chr18 49088 49090 0.000000000
## 509 chr18 49102 49104 0.000000000
## 510 chr18 49116 49118 0.000000000
## 511 chr18 49123 49125 0.000000000
## 512 chr18 49128 49130 0.000000000
## 513 chr18 49137 49139 0.000000000
## 514 chr18 49149 49151 0.000000000
## 515 chr18 49157 49159 0.000000000
## 516 chr18 49182 49184 0.000000000
## 517 chr18 49197 49199 0.000000000
## 518 chr18 49203 49205 0.000000000
## 519 chr18 49247 49249 1.000000000
## 520 chr18 49266 49268 1.000000000
## 521 chr18 49279 49281 1.000000000
## 522 chr18 49285 49287 1.000000000
## 523 chr18 49294 49296 1.000000000
## 524 chr18 49312 49314 1.000000000
## 525 chr18 49331 49333 1.000000000
## 526 chr18 49358 49360 0.000000000
## 527 chr18 49363 49365 0.000000000
## 528 chr18 49374 49376 0.028571429
## 529 chr18 49383 49385 0.028571429
## 530 chr18 49389 49391 0.028571429
## 531 chr18 49408 49410 0.217725891
## 532 chr18 49424 49426 0.381210279
## 533 chr18 49430 49432 0.601512849
## 534 chr18 49459 49461 0.601512849
## 535 chr18 49468 49470 0.601512849
## 536 chr18 49505 49507 0.601512849
## 537 chr18 49508 49510 0.601512849
## 538 chr18 49520 49522 0.366924565
## 539 chr18 49529 49531 0.366924565
## 540 chr18 49536 49538 0.366924565
## 541 chr18 49544 49546 0.207011605
## 542 chr18 49576 49578 0.023809524
## 543 chr18 49588 49590 0.023809524
## 544 chr18 49590 49592 0.023809524
## 545 chr18 49607 49609 0.085354897
## 546 chr18 49609 49611 0.085354897
## 547 chr18 49614 49616 0.189256835
## 548 chr18 49624 49626 0.339298968
## 549 chr18 49631 49633 0.339298968
## 550 chr18 49637 49639 0.824737926
## 551 chr18 49651 49653 0.824737926
## 552 chr18 49653 49655 0.824737926
## 553 chr18 49673 49675 0.824737926
## 554 chr18 49741 49743 1.573305358
## 555 chr18 49748 49750 1.573305358
## 556 chr18 49791 49793 0.222222222
## 557 chr18 49829 49831 0.222222222
## 558 chr18 49897 49899 0.000000000
## 559 chr18 49915 49917 0.000000000
## 560 chr18 50035 50037 0.000000000
## 561 chr18 50061 50063 0.000000000
## 562 chr18 50094 50096 0.000000000
## 563 chr18 50157 50159 0.000000000
## 564 chr18 50219 50221 0.000000000
## 565 chr18 50269 50271 0.000000000
## 566 chr18 50327 50329 0.000000000
## 567 chr18 50391 50393 0.000000000
## 568 chr18 50477 50479 0.000000000
## 569 chr18 50735 50737 0.000000000
## 570 chr18 50764 50766 0.000000000
## 571 chr18 51098 51100 0.000000000
## 572 chr18 51341 51343 0.500000000
## 573 chr18 51402 51404 0.500000000
## 574 chr18 51531 51533 0.467532468
## 575 chr18 51541 51543 0.467532468
## 576 chr18 51563 51565 1.129870130
## 577 chr18 51627 51629 0.467532468
## 578 chr18 51658 51660 0.467532468
## 579 chr18 51827 51829 0.000000000
## 580 chr18 52021 52023 0.000000000
## 581 chr18 52289 52291 0.000000000
## 582 chr18 52295 52297 0.000000000
## 583 chr18 52573 52575 0.000000000
## 584 chr18 52776 52778 0.000000000
## 585 chr18 52931 52933 0.000000000
## 586 chr18 52941 52943 0.000000000
## 587 chr18 52964 52966 0.000000000
## 588 chr18 53481 53483 0.000000000
## 589 chr18 53560 53562 0.000000000
## 590 chr18 53817 53819 0.000000000
## 591 chr18 54320 54322 0.000000000
## 592 chr18 54350 54352 0.000000000
## 593 chr18 54525 54527 0.000000000
## 594 chr18 55139 55141 1.000000000
## 595 chr18 55169 55171 1.000000000
## 596 chr18 55232 55234 1.000000000
## 597 chr18 55288 55290 0.000000000
## 598 chr18 55333 55335 0.000000000
## 599 chr18 55344 55346 0.000000000
## 600 chr18 55396 55398 0.000000000
## 601 chr18 55520 55522 0.000000000
## 602 chr18 56501 56503 0.000000000
## 603 chr18 57047 57049 0.000000000
## 604 chr18 57465 57467 0.000000000
## 605 chr18 57499 57501 0.000000000
## 606 chr18 57561 57563 0.000000000
## 607 chr18 58213 58215 0.000000000
## 608 chr18 58284 58286 0.000000000
## 609 chr18 58518 58520 0.000000000
## 610 chr18 58572 58574 0.000000000
## 611 chr18 58596 58598 0.000000000
## 612 chr18 59184 59186 0.000000000
## 613 chr18 59317 59319 0.000000000
## 614 chr18 59568 59570 0.500000000
## 615 chr18 59635 59637 0.500000000
## 616 chr18 59794 59796 1.028571429
## 617 chr18 59822 59824 1.942857143
## 618 chr18 59884 59886 1.028571429
## 619 chr18 60015 60017 0.000000000
## 620 chr18 60164 60166 0.000000000
## 621 chr18 61290 61292 0.000000000
## 622 chr18 61615 61617 0.000000000
## 623 chr18 62054 62056 0.000000000
## 624 chr18 62448 62450 0.300000000
## 625 chr18 62478 62480 0.548148148
## 626 chr18 62486 62488 0.902576490
## 627 chr18 62503 62505 1.416425121
## 628 chr18 62518 62520 1.416425121
## 629 chr18 62574 62576 1.416425121
## 630 chr18 62666 62668 0.500000000
## 631 chr18 62699 62701 0.500000000
## 632 chr18 62997 62999 0.000000000
## 633 chr18 63523 63525 0.500000000
## 634 chr18 63580 63582 5.500000000
## 635 chr18 63792 63794 4.230769231
## 636 chr18 63797 63799 2.769230769
## 637 chr18 64471 64473 0.166666667
## 638 chr18 64498 64500 0.733333333
## 639 chr18 64594 64596 1.700000000
## 640 chr18 64648 64650 0.200000000
## 641 chr18 64655 64657 0.200000000
## 642 chr18 64680 64682 0.000000000
## 643 chr18 64710 64712 0.000000000
## 644 chr18 64764 64766 1.000000000
## 645 chr18 64821 64823 1.000000000
## 646 chr18 65027 65029 0.000000000
## 647 chr18 65104 65106 1.000000000
## 648 chr18 65355 65357 0.000000000
## 649 chr18 65583 65585 0.000000000
## 650 chr18 65760 65762 0.000000000
## 651 chr18 65822 65824 0.000000000
## 652 chr18 65870 65872 0.000000000
## 653 chr18 65948 65950 0.000000000
## 654 chr18 66036 66038 0.000000000
## 655 chr18 66178 66180 1.000000000
## 656 chr18 66182 66184 1.000000000
## 657 chr18 66455 66457 0.000000000
## 658 chr18 66475 66477 0.000000000
## 659 chr18 66809 66811 1.000000000
## 660 chr18 66932 66934 0.200000000
## 661 chr18 67017 67019 0.800000000
## 662 chr18 67063 67065 0.800000000
## 663 chr18 67087 67089 0.200000000
## 664 chr18 67184 67186 0.200000000
## 665 chr18 67195 67197 0.200000000
## 666 chr18 67215 67217 0.200000000
## 667 chr18 67241 67243 1.066666667
## 668 chr18 67274 67276 0.333333333
## 669 chr18 67529 67531 0.000000000
## 670 chr18 67739 67741 0.000000000
## 671 chr18 67747 67749 0.000000000
## 672 chr18 67809 67811 0.083333333
## 673 chr18 67858 67860 0.348484848
## 674 chr18 67885 67887 0.348484848
## 675 chr18 67945 67947 3.255644682
## 676 chr18 67996 67998 1.454248366
## 677 chr18 68025 68027 1.454248366
## 678 chr18 68056 68058 0.055555556
## 679 chr18 68129 68131 0.000000000
## 680 chr18 68330 68332 1.000000000
## 681 chr18 68492 68494 0.000000000
## 682 chr18 68524 68526 0.000000000
## 683 chr18 68555 68557 0.000000000
## 684 chr18 68627 68629 0.000000000
## 685 chr18 68838 68840 0.000000000
## 686 chr18 68854 68856 0.000000000
## 687 chr18 68881 68883 0.000000000
## 688 chr18 69068 69070 0.000000000
## 689 chr18 69213 69215 0.333333333
## 690 chr18 69251 69253 0.746666667
## 691 chr18 69325 69327 0.847321429
## 692 chr18 69355 69357 1.239007937
## 693 chr18 69368 69370 1.239007937
## 694 chr18 69387 69389 1.239007937
## 695 chr18 69405 69407 0.832506614
## 696 chr18 69439 69441 0.523148148
## 697 chr18 69639 69641 0.000000000
## 698 chr18 69921 69923 0.781818182
## 699 chr18 69926 69928 0.781818182
## 700 chr18 69930 69932 0.781818182
## 701 chr18 69959 69961 0.781818182
## 702 chr18 69976 69978 0.781818182
## 703 chr18 70062 70064 0.590909091
## 704 chr18 70101 70103 0.250000000
## 705 chr18 70115 70117 0.250000000
## 706 chr18 70402 70404 0.000000000
## 707 chr18 70503 70505 0.290322581
## 708 chr18 70528 70530 0.841013825
## 709 chr18 70548 70550 0.841013825
## 710 chr18 70581 70583 1.259216590
## 711 chr18 70588 70590 1.259216590
## 712 chr18 70590 70592 1.259216590
## 713 chr18 70670 70672 1.125000000
## 714 chr18 70674 70676 1.125000000
## 715 chr18 70852 70854 0.583333333
## 716 chr18 70886 70888 0.583333333
## 717 chr18 70913 70915 0.583333333
## 718 chr18 70964 70966 0.650000000
## 719 chr18 71015 71017 0.200000000
## 720 chr18 71059 71061 0.200000000
## 721 chr18 71062 71064 0.200000000
## 722 chr18 71154 71156 0.500000000
## 723 chr18 71180 71182 0.500000000
## 724 chr18 71489 71491 0.900000000
## 725 chr18 71493 71495 0.900000000
## 726 chr18 71541 71543 0.200000000
## 727 chr18 71653 71655 0.000000000
## 728 chr18 71672 71674 0.000000000
## 729 chr18 71680 71682 0.000000000
## 730 chr18 71739 71741 0.310344828
## 731 chr18 71806 71808 1.094373866
## 732 chr18 71813 71815 1.094373866
## 733 chr18 71836 71838 1.456256689
## 734 chr18 71838 71840 1.456256689
## 735 chr18 71915 71917 1.061078751
## 736 chr18 71917 71919 1.061078751
## 737 chr18 71948 71950 1.337394541
## 738 chr18 71959 71961 1.949182520
## 739 chr18 72038 72040 1.822336266
## 740 chr18 72050 72052 1.357323232
## 741 chr18 72133 72135 0.000000000
## 742 chr18 72163 72165 0.000000000
## 743 chr18 72235 72237 0.000000000
## 744 chr18 72267 72269 0.000000000
## 745 chr18 72413 72415 0.000000000
## 746 chr18 72463 72465 0.000000000
## 747 chr18 72487 72489 0.000000000
## 748 chr18 72506 72508 0.000000000
## 749 chr18 72566 72568 0.335664336
## 750 chr18 72673 72675 0.753496503
## 751 chr18 72689 72691 0.753496503
## 752 chr18 72692 72694 0.753496503
## 753 chr18 72701 72703 0.320512821
## 754 chr18 72729 72731 0.083333333
## 755 chr18 72764 72766 0.000000000
## 756 chr18 72795 72797 0.000000000
## 757 chr18 72822 72824 0.035534591
## 758 chr18 72826 72828 0.035534591
## 759 chr18 72858 72860 0.213803064
## 760 chr18 72880 72882 0.300681324
## 761 chr18 72897 72899 0.950150194
## 762 chr18 72914 72916 0.950150194
## 763 chr18 72920 72922 1.132527484
## 764 chr18 72922 72924 1.132527484
## 765 chr18 72947 72949 1.770672905
## 766 chr18 72951 72953 1.770672905
## 767 chr18 72959 72961 1.770672905
## 768 chr18 72964 72966 1.520552573
## 769 chr18 73002 73004 1.353154621
## 770 chr18 73020 73022 1.156042548
## 771 chr18 73036 73038 0.812916302
## 772 chr18 73062 73064 0.427374744
## 773 chr18 73066 73068 0.426930300
## 774 chr18 73069 73071 0.426930300
## 775 chr18 73072 73074 0.559348914
## 776 chr18 73078 73080 0.321950710
## 777 chr18 73080 73082 0.321950710
## 778 chr18 73097 73099 0.620844475
## 779 chr18 73116 73118 1.150373659
## 780 chr18 73146 73148 0.888459409
## 781 chr18 73152 73154 1.039103103
## 782 chr18 73158 73160 1.205423309
## 783 chr18 73174 73176 1.389746219
## 784 chr18 73188 73190 1.578521120
## 785 chr18 73210 73212 1.357436278
## 786 chr18 73245 73247 1.004264742
## 787 chr18 73248 73250 0.636566772
## 788 chr18 73255 73257 0.636566772
## 789 chr18 73257 73259 0.617473969
## 790 chr18 73261 73263 0.610051336
## 791 chr18 73263 73265 0.610051336
## 792 chr18 73267 73269 0.610051336
## 793 chr18 73272 73274 0.610051336
## 794 chr18 73281 73283 0.610051336
## 795 chr18 73286 73288 0.785639803
## 796 chr18 73288 73290 0.998238074
## 797 chr18 73314 73316 0.653672301
## 798 chr18 73319 73321 0.871230093
## 799 chr18 73337 73339 0.871230093
## 800 chr18 73351 73353 0.731475505
## 801 chr18 73370 73372 0.806980333
## 802 chr18 73374 73376 1.045898546
## 803 chr18 73376 73378 0.888983110
## 804 chr18 73408 73410 0.676107352
## 805 chr18 73445 73447 0.372026960
## 806 chr18 73465 73467 0.141276377
## 807 chr18 73490 73492 0.273474885
## 808 chr18 73493 73495 0.273474885
## 809 chr18 73496 73498 0.273474885
## 810 chr18 73500 73502 0.273474885
## 811 chr18 73505 73507 0.273474885
## 812 chr18 73511 73513 0.273474885
## 813 chr18 73516 73518 0.160330045
## 814 chr18 73518 73520 0.160330045
## 815 chr18 73520 73522 0.160330045
## 816 chr18 73522 73524 0.077035950
## 817 chr18 73525 73527 0.077035950
## 818 chr18 73532 73534 0.077035950
## 819 chr18 73547 73549 0.077035950
## 820 chr18 73551 73553 0.077035950
## 821 chr18 73559 73561 0.021276596
## 822 chr18 73561 73563 0.021276596
## 823 chr18 73591 73593 0.021276596
## 824 chr18 73611 73613 0.021276596
## 825 chr18 73652 73654 0.041666667
## 826 chr18 73663 73665 0.170289855
## 827 chr18 73668 73670 0.170289855
## 828 chr18 73705 73707 0.648272018
## 829 chr18 73738 73740 0.995525207
## 830 chr18 73740 73742 0.995525207
## 831 chr18 73763 73765 0.995525207
## 832 chr18 73826 73828 1.541470798
## 833 chr18 73838 73840 0.716435185
## 834 chr18 73897 73899 0.709821429
## 835 chr18 73914 73916 0.709821429
## 836 chr18 73920 73922 0.709821429
## 837 chr18 73922 73924 0.709821429
## 838 chr18 73943 73945 0.442857143
## 839 chr18 73951 73953 0.442857143
## 840 chr18 74091 74093 0.071428571
## 841 chr18 74111 74113 0.296703297
## 842 chr18 74169 74171 0.941232680
## 843 chr18 74221 74223 2.515578243
## 844 chr18 74260 74262 1.551814318
## 845 chr18 74262 74264 1.551814318
## 846 chr18 74324 74326 0.357142857
## 847 chr18 74344 74346 0.357142857
## 848 chr18 74346 74348 0.357142857
## 849 chr18 74389 74391 0.000000000
## 850 chr18 74471 74473 0.000000000
## 851 chr18 74487 74489 0.000000000
## 852 chr18 74497 74499 0.000000000
## 853 chr18 74499 74501 0.000000000
## 854 chr18 74503 74505 0.000000000
## 855 chr18 74582 74584 0.000000000
## 856 chr18 74608 74610 0.000000000
## 857 chr18 74724 74726 1.666666667
## 858 chr18 74726 74728 1.666666667
## 859 chr18 74784 74786 1.666666667
## 860 chr18 74859 74861 0.000000000
## 861 chr18 74911 74913 0.000000000
## 862 chr18 74918 74920 0.000000000
## 863 chr18 74941 74943 0.000000000
## 864 chr18 74949 74951 0.000000000
## 865 chr18 74965 74967 0.000000000
## 866 chr18 75091 75093 0.000000000
## 867 chr18 75099 75101 0.000000000
## 868 chr18 75172 75174 0.000000000
## 869 chr18 75212 75214 0.090909091
## 870 chr18 75224 75226 0.090909091
## 871 chr18 75257 75259 0.090909091
## 872 chr18 75284 75286 0.363636364
## 873 chr18 75314 75316 0.363636364
## 874 chr18 75347 75349 0.363636364
## 875 chr18 75355 75357 0.363636364
## 876 chr18 75401 75403 0.607092598
## 877 chr18 75411 75413 0.222910217
## 878 chr18 75418 75420 0.222910217
## 879 chr18 75435 75437 0.222910217
## 880 chr18 75441 75443 0.222910217
## 881 chr18 75443 75445 0.222910217
## 882 chr18 75474 75476 0.222910217
## 883 chr18 75504 75506 0.222910217
## 884 chr18 75522 75524 0.052631579
## 885 chr18 75534 75536 0.052631579
## 886 chr18 75576 75578 0.119298246
## 887 chr18 75580 75582 0.119298246
## 888 chr18 75583 75585 0.119298246
## 889 chr18 75591 75593 0.267182663
## 890 chr18 75594 75596 0.267182663
## 891 chr18 75602 75604 0.267182663
## 892 chr18 75610 75612 0.267182663
## 893 chr18 75619 75621 0.267182663
## 894 chr18 75650 75652 0.267182663
## 895 chr18 75656 75658 0.267182663
## 896 chr18 75662 75664 0.267182663
## 897 chr18 75691 75693 0.111455108
## 898 chr18 75713 75715 0.310039805
## 899 chr18 75717 75719 0.310039805
## 900 chr18 75733 75735 0.154061625
## 901 chr18 75751 75753 0.047619048
## 902 chr18 75758 75760 0.047619048
## 903 chr18 75760 75762 0.047619048
## 904 chr18 75763 75765 0.047619048
## 905 chr18 75765 75767 0.047619048
## 906 chr18 75769 75771 0.047619048
## 907 chr18 75774 75776 0.047619048
## 908 chr18 75776 75778 0.047619048
## 909 chr18 75788 75790 0.047619048
## 910 chr18 75821 75823 0.047619048
## 911 chr18 75824 75826 0.047619048
## 912 chr18 75839 75841 0.047619048
## 913 chr18 75844 75846 0.047619048
## 914 chr18 75863 75865 0.000000000
## 915 chr18 75867 75869 0.000000000
## 916 chr18 75884 75886 0.029411765
## 917 chr18 75892 75894 0.029411765
## 918 chr18 75901 75903 0.029411765
## 919 chr18 75929 75931 0.029411765
## 920 chr18 75951 75953 0.115966387
## 921 chr18 75954 75956 0.115966387
## 922 chr18 75957 75959 0.115966387
## 923 chr18 75960 75962 0.115966387
## 924 chr18 75964 75966 0.115966387
## 925 chr18 75969 75971 0.115966387
## 926 chr18 75976 75978 0.115966387
## 927 chr18 75980 75982 0.115966387
## 928 chr18 75982 75984 0.115966387
## 929 chr18 75984 75986 0.115966387
## 930 chr18 75986 75988 0.115966387
## 931 chr18 75988 75990 0.115966387
## 932 chr18 75996 75998 0.115966387
## 933 chr18 76011 76013 0.115966387
## 934 chr18 76015 76017 0.115966387
## 935 chr18 76023 76025 0.028571429
## 936 chr18 76025 76027 0.028571429
## 937 chr18 76055 76057 0.028571429
## 938 chr18 76074 76076 0.028571429
## 939 chr18 76091 76093 0.028571429
## 940 chr18 76107 76109 0.000000000
## 941 chr18 76125 76127 0.000000000
## 942 chr18 76168 76170 1.000000000
## 943 chr18 76201 76203 1.000000000
## 944 chr18 76224 76226 1.000000000
## 945 chr18 76228 76230 1.000000000
## 946 chr18 76246 76248 1.000000000
## 947 chr18 76259 76261 1.000000000
## 948 chr18 76298 76300 0.000000000
## 949 chr18 76300 76302 0.000000000
## 950 chr18 76344 76346 0.000000000
## 951 chr18 76354 76356 0.000000000
## 952 chr18 76361 76363 0.000000000
## 953 chr18 76416 76418 0.000000000
## 954 chr18 76524 76526 0.000000000
## 955 chr18 76589 76591 0.000000000
## 956 chr18 76651 76653 0.000000000
## 957 chr18 76813 76815 0.000000000
## 958 chr18 77123 77125 0.000000000
## 959 chr18 77266 77268 0.000000000
## 960 chr18 77485 77487 0.000000000
## 961 chr18 77853 77855 1.000000000
## 962 chr18 77908 77910 1.000000000
## 963 chr18 78001 78003 0.000000000
## 964 chr18 78065 78067 0.000000000
## 965 chr18 78082 78084 0.000000000
## 966 chr18 78102 78104 0.000000000
## 967 chr18 78122 78124 0.000000000
## 968 chr18 78147 78149 0.000000000
## 969 chr18 78202 78204 0.000000000
## 970 chr18 78247 78249 0.000000000
## 971 chr18 78345 78347 1.000000000
## 972 chr18 78359 78361 1.000000000
## 973 chr18 78408 78410 1.000000000
## 974 chr18 78531 78533 0.000000000
## 975 chr18 78740 78742 0.000000000
## 976 chr18 78760 78762 0.000000000
## 977 chr18 78768 78770 0.000000000
## 978 chr18 78785 78787 0.000000000
## 979 chr18 79224 79226 0.000000000
## 980 chr18 79294 79296 0.000000000
## 981 chr18 79364 79366 0.000000000
## 982 chr18 79434 79436 0.000000000
## 983 chr18 79502 79504 0.000000000
## 984 chr18 79536 79538 0.000000000
## 985 chr18 79604 79606 0.000000000
## 986 chr18 79627 79629 0.000000000
## 987 chr18 79908 79910 1.000000000
## 988 chr18 79969 79971 1.000000000
## 989 chr18 80077 80079 0.000000000
## 990 chr18 80166 80168 0.444444444
## 991 chr18 80193 80195 0.966666667
## 992 chr18 80247 80249 1.688888889
## 993 chr18 80333 80335 0.975000000
## 994 chr18 80371 80373 1.050000000
## 995 chr18 80394 80396 0.500000000
## 996 chr18 80448 80450 2.375000000
## 997 chr18 80596 80598 0.000000000
## 998 chr18 80650 80652 0.500000000
## 999 chr18 80709 80711 0.500000000
## 1000 chr18 80947 80949 19.000000000
## 1001 chr18 81276 81278 3.145454545
## 1002 chr18 81316 81318 1.787878788
## 1003 chr18 81350 81352 1.066666667
## 1004 chr18 81469 81471 0.000000000
## 1005 chr18 81501 81503 0.000000000
## 1006 chr18 81519 81521 0.000000000
## 1007 chr18 81635 81637 0.000000000
## 1008 chr18 81649 81651 0.000000000
## 1009 chr18 81805 81807 0.000000000
## 1010 chr18 81807 81809 0.000000000
## 1011 chr18 82026 82028 0.000000000
## 1012 chr18 82114 82116 0.000000000
## 1013 chr18 82157 82159 0.000000000
## 1014 chr18 82318 82320 0.619047619
## 1015 chr18 82358 82360 0.619047619
## 1016 chr18 82366 82368 0.619047619
## 1017 chr18 82412 82414 0.142857143
## 1018 chr18 82450 82452 0.000000000
## 1019 chr18 82483 82485 0.000000000
## 1020 chr18 82517 82519 0.000000000
## 1021 chr18 82578 82580 0.400000000
## 1022 chr18 82581 82583 0.400000000
## 1023 chr18 82589 82591 0.400000000
## 1024 chr18 82630 82632 0.400000000
## 1025 chr18 82652 82654 0.400000000
## 1026 chr18 82785 82787 0.000000000
## 1027 chr18 82880 82882 0.884057971
## 1028 chr18 82907 82909 1.260869565
## 1029 chr18 82909 82911 1.260869565
## 1030 chr18 82930 82932 1.260869565
## 1031 chr18 82975 82977 2.333333333
## 1032 chr18 83021 83023 3.000000000
## 1033 chr18 83141 83143 0.685714286
## 1034 chr18 83153 83155 1.528571429
## 1035 chr18 83214 83216 0.619047619
## 1036 chr18 83290 83292 0.166666667
## 1037 chr18 83396 83398 0.000000000
## 1038 chr18 83451 83453 0.000000000
## 1039 chr18 83502 83504 0.000000000
## 1040 chr18 83557 83559 0.000000000
## 1041 chr18 83608 83610 0.000000000
## 1042 chr18 83668 83670 0.000000000
## 1043 chr18 83722 83724 0.000000000
## 1044 chr18 83735 83737 1.000000000
## 1045 chr18 83754 83756 1.000000000
## 1046 chr18 83854 83856 1.000000000
## 1047 chr18 83868 83870 1.000000000
## 1048 chr18 83916 83918 0.000000000
## 1049 chr18 83926 83928 0.000000000
## 1050 chr18 84002 84004 0.000000000
## 1051 chr18 84022 84024 0.000000000
## 1052 chr18 84047 84049 0.000000000
## 1053 chr18 84071 84073 0.000000000
## 1054 chr18 84149 84151 1.000000000
## 1055 chr18 84181 84183 1.000000000
## 1056 chr18 84225 84227 1.000000000
## 1057 chr18 84429 84431 1.000000000
## 1058 chr18 84706 84708 2.039845261
## 1059 chr18 84721 84723 2.039845261
## 1060 chr18 84755 84757 1.773760438
## 1061 chr18 84770 84772 1.473838138
## 1062 chr18 84786 84788 1.473838138
## 1063 chr18 84805 84807 2.018067905
## 1064 chr18 84815 84817 1.623625372
## 1065 chr18 84882 84884 0.280256410
## 1066 chr18 84908 84910 0.354817814
## 1067 chr18 84922 84924 0.185263158
## 1068 chr18 84981 84983 0.498725074
## 1069 chr18 84987 84989 0.498725074
## 1070 chr18 85010 85012 1.063877084
## 1071 chr18 85036 85038 2.809312684
## 1072 chr18 85047 85049 3.433993952
## 1073 chr18 85094 85096 3.643517762
## 1074 chr18 85187 85189 4.629270186
## 1075 chr18 85228 85230 3.072463768
## 1076 chr18 85277 85279 1.086956522
## 1077 chr18 85503 85505 1.000000000
## 1078 chr18 85687 85689 0.000000000
## 1079 chr18 85695 85697 0.000000000
## 1080 chr18 85931 85933 0.000000000
## 1081 chr18 86110 86112 0.000000000
## 1082 chr18 86161 86163 0.000000000
## 1083 chr18 86222 86224 0.000000000
## 1084 chr18 86314 86316 0.000000000
## 1085 chr18 86413 86415 0.000000000
## 1086 chr18 86522 86524 0.000000000
## 1087 chr18 86583 86585 0.000000000
## 1088 chr18 86746 86748 1.500000000
## 1089 chr18 86850 86852 1.166666667
## 1090 chr18 86931 86933 0.333333333
## 1091 chr18 86957 86959 0.000000000
## 1092 chr18 86977 86979 0.000000000
## 1093 chr18 87012 87014 0.000000000
## 1094 chr18 87071 87073 0.000000000
## 1095 chr18 87150 87152 0.000000000
## 1096 chr18 87152 87154 0.000000000
## 1097 chr18 87311 87313 0.000000000
## 1098 chr18 87400 87402 0.000000000
## 1099 chr18 87614 87616 0.000000000
## 1100 chr18 87630 87632 0.000000000
## 1101 chr18 87652 87654 0.000000000
## 1102 chr18 87660 87662 0.000000000
## 1103 chr18 87690 87692 1.000000000
## 1104 chr18 87694 87696 1.000000000
## 1105 chr18 87740 87742 1.000000000
## 1106 chr18 87791 87793 1.000000000
## 1107 chr18 87811 87813 1.000000000
## 1108 chr18 87843 87845 0.000000000
## 1109 chr18 87880 87882 0.000000000
## 1110 chr18 88031 88033 0.000000000
## 1111 chr18 88067 88069 0.000000000
## 1112 chr18 88145 88147 0.000000000
## 1113 chr18 88216 88218 0.000000000
## 1114 chr18 88232 88234 0.000000000
## 1115 chr18 88306 88308 0.000000000
## 1116 chr18 88341 88343 0.000000000
## 1117 chr18 88354 88356 0.000000000
## 1118 chr18 88395 88397 0.000000000
## 1119 chr18 88401 88403 0.000000000
## 1120 chr18 88475 88477 0.666666667
## 1121 chr18 88497 88499 0.666666667
## 1122 chr18 88512 88514 0.666666667
## 1123 chr18 88647 88649 0.000000000
## 1124 chr18 88698 88700 0.000000000
## 1125 chr18 88821 88823 0.000000000
## 1126 chr18 88839 88841 0.000000000
## 1127 chr18 88981 88983 0.000000000
## 1128 chr18 89150 89152 0.666666667
## 1129 chr18 89165 89167 0.666666667
## 1130 chr18 89233 89235 0.666666667
## 1131 chr18 89343 89345 0.666666667
## 1132 chr18 89361 89363 0.666666667
## 1133 chr18 89372 89374 0.666666667
## 1134 chr18 89546 89548 0.000000000
## 1135 chr18 89602 89604 0.000000000
## 1136 chr18 89634 89636 0.000000000
## 1137 chr18 89696 89698 0.000000000
## 1138 chr18 89740 89742 0.000000000
## 1139 chr18 89756 89758 0.000000000
## 1140 chr18 89808 89810 0.000000000
## 1141 chr18 89832 89834 0.000000000
## 1142 chr18 89838 89840 0.000000000
## 1143 chr18 90062 90064 0.000000000
## 1144 chr18 90104 90106 0.000000000
## 1145 chr18 90174 90176 0.333333333
## 1146 chr18 90184 90186 0.333333333
## 1147 chr18 90241 90243 0.333333333
## 1148 chr18 90333 90335 0.200000000
## 1149 chr18 90336 90338 0.200000000
## 1150 chr18 90360 90362 0.200000000
## 1151 chr18 90413 90415 0.685714286
## 1152 chr18 90472 90474 0.507936508
## 1153 chr18 90534 90536 0.949404762
## 1154 chr18 90572 90574 1.165032680
## 1155 chr18 90596 90598 0.540441176
## 1156 chr18 90626 90628 0.540441176
## 1157 chr18 90662 90664 0.540441176
## 1158 chr18 90674 90676 0.235294118
## 1159 chr18 90696 90698 0.235294118
## 1160 chr18 90788 90790 0.000000000
## 1161 chr18 90800 90802 0.000000000
## 1162 chr18 90822 90824 0.250000000
## 1163 chr18 90840 90842 0.250000000
## 1164 chr18 90869 90871 1.141025641
## 1165 chr18 90897 90899 1.141025641
## 1166 chr18 90905 90907 1.141025641
## 1167 chr18 90999 91001 0.076923077
## 1168 chr18 91288 91290 0.500000000
## 1169 chr18 91360 91362 0.500000000
## 1170 chr18 91483 91485 0.000000000
## 1171 chr18 91799 91801 0.000000000
## 1172 chr18 92085 92087 0.000000000
## 1173 chr18 92125 92127 0.000000000
## 1174 chr18 92210 92212 0.000000000
## 1175 chr18 92228 92230 0.000000000
## 1176 chr18 92359 92361 0.000000000
## 1177 chr18 92412 92414 0.000000000
## 1178 chr18 92505 92507 0.000000000
## 1179 chr18 92551 92553 0.000000000
## 1180 chr18 92701 92703 0.000000000
## 1181 chr18 92928 92930 0.000000000
## 1182 chr18 92932 92934 0.000000000
## 1183 chr18 93005 93007 0.000000000
## 1184 chr18 93014 93016 0.000000000
## 1185 chr18 93157 93159 0.000000000
## 1186 chr18 93187 93189 0.000000000
## 1187 chr18 93195 93197 0.000000000
## 1188 chr18 93238 93240 0.000000000
## 1189 chr18 93362 93364 0.000000000
## 1190 chr18 93555 93557 0.000000000
## 1191 chr18 93578 93580 0.000000000
## 1192 chr18 93597 93599 0.076923077
## 1193 chr18 93607 93609 0.076923077
## 1194 chr18 93640 93642 0.076923077
## 1195 chr18 93651 93653 0.320512821
## 1196 chr18 93690 93692 0.320512821
## 1197 chr18 93723 93725 0.320512821
## 1198 chr18 93735 93737 0.320512821
## 1199 chr18 93739 93741 0.320512821
## 1200 chr18 93759 93761 0.083333333
## 1201 chr18 93783 93785 0.083333333
## 1202 chr18 93821 93823 0.000000000
## 1203 chr18 93831 93833 0.000000000
## 1204 chr18 93976 93978 0.500000000
## 1205 chr18 94064 94066 0.500000000
## 1206 chr18 94128 94130 2.000000000
## 1207 chr18 94211 94213 2.000000000
## 1208 chr18 94260 94262 0.000000000
## 1209 chr18 94298 94300 0.000000000
## 1210 chr18 94426 94428 0.500000000
## 1211 chr18 94464 94466 0.500000000
## 1212 chr18 94703 94705 0.333333333
## 1213 chr18 94739 94741 0.866666667
## 1214 chr18 94811 94813 0.400000000
## 1215 chr18 94840 94842 0.400000000
## 1216 chr18 94869 94871 0.400000000
## 1217 chr18 94873 94875 0.400000000
## 1218 chr18 94885 94887 0.100000000
## 1219 chr18 94937 94939 0.100000000
## 1220 chr18 94991 94993 0.000000000
## 1221 chr18 95335 95337 0.000000000
## 1222 chr18 95368 95370 0.000000000
## 1223 chr18 95455 95457 0.285714286
## 1224 chr18 95487 95489 0.659340659
## 1225 chr18 95492 95494 0.659340659
## 1226 chr18 95516 95518 0.659340659
## 1227 chr18 95537 95539 0.659340659
## 1228 chr18 95600 95602 0.076923077
## 1229 chr18 95708 95710 0.143939394
## 1230 chr18 95717 95719 0.143939394
## 1231 chr18 95724 95726 0.319357367
## 1232 chr18 95735 95737 0.319357367
## 1233 chr18 95744 95746 0.319357367
## 1234 chr18 95763 95765 0.319357367
## 1235 chr18 95766 95768 0.319357367
## 1236 chr18 95790 95792 0.701753803
## 1237 chr18 95835 95837 1.584693643
## 1238 chr18 95893 95895 1.296703510
## 1239 chr18 95904 95906 1.296703510
## 1240 chr18 95914 95916 1.296703510
## 1241 chr18 95922 95924 1.296703510
## 1242 chr18 95928 95930 1.296703510
## 1243 chr18 95945 95947 0.549968065
## 1244 chr18 95957 95959 0.549968065
## 1245 chr18 95973 95975 0.245433255
## 1246 chr18 96055 96057 0.000000000
## 1247 chr18 96099 96101 0.000000000
## 1248 chr18 96171 96173 0.513599367
## 1249 chr18 96175 96177 0.513599367
## 1250 chr18 96188 96190 1.802828781
## 1251 chr18 96219 96221 2.176094115
## 1252 chr18 96264 96266 2.613920853
## 1253 chr18 96301 96303 1.718688197
## 1254 chr18 96310 96312 1.377008056
## 1255 chr18 96316 96318 1.377008056
## 1256 chr18 96329 96331 0.636777017
## 1257 chr18 96364 96366 0.087619048
## 1258 chr18 96401 96403 0.087619048
## 1259 chr18 96414 96416 0.180952381
## 1260 chr18 96421 96423 0.180952381
## 1261 chr18 96445 96447 0.066666667
## 1262 chr18 96467 96469 0.066666667
## 1263 chr18 96469 96471 0.066666667
## 1264 chr18 96481 96483 0.066666667
## 1265 chr18 96488 96490 0.066666667
## 1266 chr18 96492 96494 0.355555556
## 1267 chr18 96497 96499 0.355555556
## 1268 chr18 96532 96534 0.355555556
## 1269 chr18 96564 96566 0.111111111
## 1270 chr18 96570 96572 0.111111111
## 1271 chr18 96637 96639 0.111111111
## 1272 chr18 96652 96654 0.000000000
## 1273 chr18 96657 96659 0.000000000
## 1274 chr18 96667 96669 0.000000000
## 1275 chr18 96678 96680 0.000000000
## 1276 chr18 96687 96689 0.000000000
## 1277 chr18 96689 96691 0.000000000
## 1278 chr18 96702 96704 0.000000000
## 1279 chr18 96707 96709 0.000000000
## 1280 chr18 96712 96714 0.000000000
## 1281 chr18 96721 96723 0.000000000
## 1282 chr18 96732 96734 0.000000000
## 1283 chr18 96736 96738 0.000000000
## 1284 chr18 96764 96766 0.000000000
## 1285 chr18 96780 96782 0.000000000
## 1286 chr18 96793 96795 0.000000000
## 1287 chr18 96824 96826 0.000000000
## 1288 chr18 96840 96842 0.000000000
## 1289 chr18 96853 96855 0.000000000
## 1290 chr18 96884 96886 0.000000000
## 1291 chr18 96900 96902 0.000000000
## 1292 chr18 96913 96915 0.000000000
## 1293 chr18 96917 96919 0.000000000
## 1294 chr18 96945 96947 0.000000000
## 1295 chr18 96961 96963 0.000000000
## 1296 chr18 96974 96976 0.000000000
## 1297 chr18 97005 97007 0.000000000
## 1298 chr18 97021 97023 0.000000000
## 1299 chr18 97034 97036 0.000000000
## 1300 chr18 97065 97067 0.000000000
## 1301 chr18 97081 97083 0.000000000
## 1302 chr18 97094 97096 0.000000000
## 1303 chr18 97098 97100 0.000000000
## 1304 chr18 97126 97128 0.000000000
## 1305 chr18 97142 97144 0.000000000
## 1306 chr18 97155 97157 0.000000000
## 1307 chr18 97186 97188 0.000000000
## 1308 chr18 97202 97204 0.000000000
## 1309 chr18 97215 97217 0.000000000
## 1310 chr18 97219 97221 0.000000000
## 1311 chr18 97247 97249 0.000000000
## 1312 chr18 97263 97265 0.000000000
## 1313 chr18 97276 97278 0.000000000
## 1314 chr18 97280 97282 0.000000000
## 1315 chr18 97308 97310 0.000000000
## 1316 chr18 97324 97326 0.000000000
## 1317 chr18 97337 97339 0.000000000
## 1318 chr18 97341 97343 0.000000000
## 1319 chr18 97369 97371 0.148965517
## 1320 chr18 97385 97387 0.148965517
## 1321 chr18 97398 97400 0.148965517
## 1322 chr18 97402 97404 0.148965517
## 1323 chr18 97430 97432 0.148965517
## 1324 chr18 97446 97448 0.972413793
## 1325 chr18 97459 97461 0.972413793
## 1326 chr18 97501 97503 0.972413793
## 1327 chr18 97506 97508 0.617931034
## 1328 chr18 97519 97521 0.360000000
## 1329 chr18 97574 97576 0.360000000
## 1330 chr18 97608 97610 0.000000000
## 1331 chr18 97635 97637 0.000000000
## 1332 chr18 97641 97643 0.000000000
## 1333 chr18 97663 97665 0.000000000
## 1334 chr18 97686 97688 0.000000000
## 1335 chr18 97692 97694 0.000000000
## 1336 chr18 97792 97794 0.259109312
## 1337 chr18 97821 97823 0.546558704
## 1338 chr18 97850 97852 0.978744939
## 1339 chr18 97854 97856 0.978744939
## 1340 chr18 97865 97867 0.503289474
## 1341 chr18 97870 97872 0.503289474
## 1342 chr18 97885 97887 0.230263158
## 1343 chr18 98289 98291 0.000000000
## 1344 chr18 98439 98441 0.000000000
## 1345 chr18 98765 98767 1.000000000
## 1346 chr18 98777 98779 1.000000000
## 1347 chr18 98968 98970 0.000000000
## 1348 chr18 99052 99054 0.000000000
## 1349 chr18 99265 99267 0.000000000
## 1350 chr18 99311 99313 0.000000000
## 1351 chr18 99640 99642 0.333333333
## 1352 chr18 99774 99776 1.066666667
## 1353 chr18 99792 99794 0.200000000
## 1354 chr18 99803 99805 0.200000000
## 1355 chr18 99854 99856 0.200000000
## 1356 chr18 99897 99899 0.000000000
## 1357 chr18 99949 99951 0.000000000
## 1358 chr18 99976 99978 0.250000000
## 1359 chr18 100002 100004 0.250000000
## 1360 chr18 100044 100046 0.250000000
## 1361 chr18 100058 100060 0.250000000
## 1362 chr18 100183 100185 1.000000000
## 1363 chr18 100826 100828 1.000000000
## 1364 chr18 100977 100979 0.000000000
## 1365 chr18 101102 101104 1.000000000
## 1366 chr18 101280 101282 0.000000000
## 1367 chr18 101505 101507 0.000000000
## 1368 chr18 101553 101555 0.000000000
## 1369 chr18 101588 101590 0.000000000
## 1370 chr18 101698 101700 0.000000000
## 1371 chr18 101761 101763 0.000000000
## 1372 chr18 101872 101874 0.000000000
## 1373 chr18 101942 101944 0.000000000
## 1374 chr18 102195 102197 0.000000000
## 1375 chr18 102237 102239 0.000000000
## 1376 chr18 102288 102290 0.000000000
## 1377 chr18 102806 102808 0.000000000
## 1378 chr18 102845 102847 0.000000000
## 1379 chr18 102874 102876 0.000000000
## 1380 chr18 102922 102924 0.000000000
## 1381 chr18 102983 102985 0.000000000
## 1382 chr18 102995 102997 0.000000000
## 1383 chr18 103524 103526 0.000000000
## 1384 chr18 103576 103578 0.000000000
## 1385 chr18 103722 103724 0.200000000
## 1386 chr18 103724 103726 0.200000000
## 1387 chr18 103762 103764 0.200000000
## 1388 chr18 103792 103794 0.200000000
## 1389 chr18 103823 103825 0.200000000
## 1390 chr18 103853 103855 0.166666667
## 1391 chr18 103865 103867 0.166666667
## 1392 chr18 103869 103871 0.166666667
## 1393 chr18 103897 103899 0.166666667
## 1394 chr18 103945 103947 0.166666667
## 1395 chr18 103971 103973 0.166666667
## 1396 chr18 104342 104344 0.000000000
## 1397 chr18 104494 104496 0.000000000
## 1398 chr18 104522 104524 0.000000000
## 1399 chr18 104598 104600 0.000000000
## 1400 chr18 104681 104683 0.000000000
## 1401 chr18 105025 105027 0.000000000
## 1402 chr18 105374 105376 2.272727273
## 1403 chr18 105443 105445 0.431818182
## 1404 chr18 105475 105477 1.147727273
## 1405 chr18 105481 105483 1.147727273
## 1406 chr18 105670 105672 4.000000000
## 1407 chr18 105872 105874 0.000000000
## 1408 chr18 105969 105971 0.000000000
## 1409 chr18 106343 106345 0.000000000
## 1410 chr18 106372 106374 0.000000000
## 1411 chr18 106555 106557 0.000000000
## 1412 chr18 106748 106750 5.000000000
## 1413 chr18 106942 106944 2.000000000
## 1414 chr18 107235 107237 1.000000000
## 1415 chr18 107486 107488 12.179688350
## 1416 chr18 107507 107509 16.583251873
## 1417 chr18 107540 107542 14.795794279
## 1418 chr18 107589 107591 6.840553745
## 1419 chr18 107632 107634 3.600711754
## 1420 chr18 108155 108157 36.738372093
## 1421 chr18 108222 108224 72.261627907
## 1422 chr18 108540 108542 10.000000000
## 1423 chr18 108747 108749 4.229465450
## 1424 chr18 108775 108777 7.611212516
## 1425 chr18 108889 108891 29.159322034
## 1426 chr18 109082 109084 4.400000000
## 1427 chr18 109146 109148 1.600000000
## 1428 chr18 109283 109285 25.000000000
## 1429 chr18 109490 109492 12.392123288
## 1430 chr18 109510 109512 7.101027397
## 1431 chr18 109566 109568 11.052303861
## 1432 chr18 109643 109645 3.454545455
## 1433 chr18 109859 109861 7.000000000
## 1434 chr18 110008 110010 14.599303136
## 1435 chr18 110023 110025 5.382839721
## 1436 chr18 110033 110035 4.017857143
## 1437 chr18 110112 110114 0.000000000
## 1438 chr18 110172 110174 0.000000000
## 1439 chr18 110771 110773 18.222222222
## 1440 chr18 110839 110841 8.177777778
## 1441 chr18 110921 110923 7.600000000
## 1442 chr18 111061 111063 5.000000000
## 1443 chr18 111263 111265 0.000000000
## 1444 chr18 111398 111400 18.809523810
## 1445 chr18 111498 111500 0.190476190
## 1446 chr18 111675 111677 1.019379845
## 1447 chr18 111678 111680 1.019379845
## 1448 chr18 111713 111715 0.621943948
## 1449 chr18 111741 111743 0.216457961
## 1450 chr18 111755 111757 0.342664668
## 1451 chr18 111762 111764 0.342664668
## 1452 chr18 111769 111771 0.494997502
## 1453 chr18 111776 111778 0.494997502
## 1454 chr18 111778 111780 0.494997502
## 1455 chr18 111798 111800 0.494997502
## 1456 chr18 111825 111827 0.271489951
## 1457 chr18 111829 111831 0.126694387
## 1458 chr18 111836 111838 0.126694387
## 1459 chr18 111841 111843 0.126694387
## 1460 chr18 111853 111855 0.126694387
## 1461 chr18 111861 111863 0.126694387
## 1462 chr18 111871 111873 0.126694387
## 1463 chr18 111875 111877 0.245848926
## 1464 chr18 111879 111881 0.245848926
## 1465 chr18 111883 111885 0.245848926
## 1466 chr18 111886 111888 0.245848926
## 1467 chr18 111892 111894 0.245848926
## 1468 chr18 111894 111896 0.245848926
## 1469 chr18 111900 111902 0.143846154
## 1470 chr18 111911 111913 0.143846154
## 1471 chr18 111916 111918 0.143846154
## 1472 chr18 111919 111921 0.069230769
## 1473 chr18 111939 111941 0.069230769
## 1474 chr18 111944 111946 0.069230769
## 1475 chr18 111946 111948 0.069230769
## 1476 chr18 111952 111954 0.069230769
## 1477 chr18 111955 111957 0.019230769
## 1478 chr18 111960 111962 0.019230769
## 1479 chr18 111962 111964 0.019230769
## 1480 chr18 111967 111969 0.019230769
## 1481 chr18 111984 111986 0.019230769
## 1482 chr18 111993 111995 0.019230769
## 1483 chr18 111996 111998 0.019230769
## 1484 chr18 111998 112000 0.019230769
## 1485 chr18 112005 112007 0.019230769
## 1486 chr18 112043 112045 0.000000000
## 1487 chr18 112046 112048 0.000000000
## 1488 chr18 112048 112050 0.000000000
## 1489 chr18 112055 112057 0.000000000
## 1490 chr18 112061 112063 0.000000000
## 1491 chr18 112085 112087 0.000000000
## 1492 chr18 112093 112095 0.000000000
## 1493 chr18 112096 112098 0.000000000
## 1494 chr18 112106 112108 0.000000000
## 1495 chr18 112117 112119 0.000000000
## 1496 chr18 112133 112135 0.003773585
## 1497 chr18 112154 112156 0.458176101
## 1498 chr18 112162 112164 1.098560254
## 1499 chr18 112170 112172 1.853142488
## 1500 chr18 112172 112174 2.032811922
## 1501 chr18 112174 112176 2.438935974
## 1502 chr18 112178 112180 2.438935974
## 1503 chr18 112187 112189 2.950834502
## 1504 chr18 112211 112213 2.950834502
## 1505 chr18 112226 112228 2.950834502
## 1506 chr18 112256 112258 3.663112315
## 1507 chr18 112276 112278 4.604629639
## 1508 chr18 112309 112311 1.615448114
## 1509 chr18 112318 112320 0.681049719
## 1510 chr18 112330 112332 0.225133100
## 1511 chr18 112335 112337 0.156985093
## 1512 chr18 112343 112345 0.156985093
## 1513 chr18 112351 112353 0.156985093
## 1514 chr18 112372 112374 0.156985093
## 1515 chr18 112374 112376 0.156985093
## 1516 chr18 112389 112391 0.156985093
## 1517 chr18 112399 112401 0.091876751
## 1518 chr18 112408 112410 0.000000000
## 1519 chr18 112414 112416 0.000000000
## 1520 chr18 112425 112427 0.000000000
## 1521 chr18 112427 112429 0.000000000
## 1522 chr18 112453 112455 0.000000000
## 1523 chr18 112466 112468 0.000000000
## 1524 chr18 112485 112487 0.000000000
## 1525 chr18 112490 112492 0.000000000
## 1526 chr18 112500 112502 0.000000000
## 1527 chr18 112518 112520 0.000000000
## 1528 chr18 112527 112529 0.000000000
## 1529 chr18 112885 112887 0.000000000
## 1530 chr18 112891 112893 0.000000000
## 1531 chr18 112929 112931 0.000000000
## 1532 chr18 112992 112994 0.000000000
## 1533 chr18 113024 113026 0.000000000
## 1534 chr18 113036 113038 0.000000000
## 1535 chr18 113112 113114 0.000000000
## 1536 chr18 113120 113122 0.000000000
## 1537 chr18 113133 113135 0.000000000
## 1538 chr18 113151 113153 0.000000000
## 1539 chr18 113272 113274 0.000000000
## 1540 chr18 113649 113651 0.000000000
## 1541 chr18 114102 114104 1.000000000
## 1542 chr18 114183 114185 1.000000000
## 1543 chr18 114226 114228 0.000000000
## 1544 chr18 114352 114354 0.000000000
## 1545 chr18 114370 114372 0.000000000
## 1546 chr18 114434 114436 0.000000000
## 1547 chr18 114466 114468 0.000000000
## 1548 chr18 114488 114490 0.000000000
## 1549 chr18 114514 114516 0.000000000
## 1550 chr18 114548 114550 0.000000000
## 1551 chr18 114560 114562 0.000000000
## 1552 chr18 114851 114853 0.000000000
## 1553 chr18 115171 115173 0.000000000
## 1554 chr18 115931 115933 0.000000000
## 1555 chr18 115964 115966 0.000000000
## 1556 chr18 115991 115993 0.000000000
## 1557 chr18 116022 116024 0.000000000
## 1558 chr18 116042 116044 0.000000000
## 1559 chr18 116853 116855 0.000000000
## 1560 chr18 116963 116965 0.000000000
## 1561 chr18 117240 117242 0.000000000
## 1562 chr18 117527 117529 0.000000000
## 1563 chr18 117549 117551 0.000000000
## 1564 chr18 117633 117635 0.000000000
## 1565 chr18 117649 117651 0.000000000
## 1566 chr18 117707 117709 0.000000000
## 1567 chr18 117739 117741 0.000000000
## 1568 chr18 117781 117783 0.000000000
## 1569 chr18 117785 117787 0.000000000
## 1570 chr18 118418 118420 0.000000000
## 1571 chr18 118434 118436 0.000000000
## 1572 chr18 118469 118471 0.000000000
## 1573 chr18 118524 118526 0.000000000
## 1574 chr18 119023 119025 0.000000000
## 1575 chr18 119112 119114 0.000000000
## 1576 chr18 119132 119134 0.000000000
## 1577 chr18 119180 119182 1.000000000
## 1578 chr18 119338 119340 0.000000000
## 1579 chr18 119358 119360 0.000000000
## 1580 chr18 119429 119431 0.000000000
## 1581 chr18 119442 119444 0.000000000
## 1582 chr18 119451 119453 0.000000000
## 1583 chr18 119574 119576 0.000000000
## 1584 chr18 119717 119719 0.250000000
## 1585 chr18 119747 119749 0.250000000
## 1586 chr18 119831 119833 0.900000000
## 1587 chr18 119886 119888 1.145454545
## 1588 chr18 119956 119958 0.363636364
## 1589 chr18 119966 119968 1.045454545
## 1590 chr18 119976 119978 1.045454545
## 1591 chr18 120215 120217 0.000000000
## 1592 chr18 120250 120252 0.000000000
## 1593 chr18 120644 120646 0.000000000
## 1594 chr18 120713 120715 0.000000000
## 1595 chr18 120730 120732 0.000000000
## 1596 chr18 120878 120880 0.000000000
## 1597 chr18 120880 120882 0.000000000
## 1598 chr18 121011 121013 0.000000000
## 1599 chr18 121073 121075 0.000000000
## 1600 chr18 121366 121368 0.000000000
## 1601 chr18 121718 121720 0.000000000
## 1602 chr18 121947 121949 1.000000000
## 1603 chr18 122070 122072 0.000000000
## 1604 chr18 122074 122076 0.000000000
## 1605 chr18 122116 122118 0.000000000
## 1606 chr18 122346 122348 0.000000000
## 1607 chr18 122554 122556 0.000000000
## 1608 chr18 122588 122590 0.000000000
## 1609 chr18 122823 122825 0.000000000
## 1610 chr18 123310 123312 0.000000000
## 1611 chr18 123576 123578 0.000000000
## 1612 chr18 123784 123786 0.000000000
## 1613 chr18 123969 123971 0.000000000
## 1614 chr18 123977 123979 0.000000000
## 1615 chr18 124008 124010 0.000000000
## 1616 chr18 124010 124012 0.000000000
## 1617 chr18 124016 124018 0.000000000
## 1618 chr18 124033 124035 0.000000000
## 1619 chr18 124072 124074 0.000000000
## 1620 chr18 124239 124241 0.000000000
## 1621 chr18 124241 124243 0.000000000
## 1622 chr18 124294 124296 0.000000000
## 1623 chr18 124352 124354 0.000000000
## 1624 chr18 124510 124512 0.000000000
## 1625 chr18 124934 124936 0.000000000
## 1626 chr18 125237 125239 0.153846154
## 1627 chr18 125241 125243 0.153846154
## 1628 chr18 125245 125247 0.153846154
## 1629 chr18 125247 125249 0.153846154
## 1630 chr18 125257 125259 0.153846154
## 1631 chr18 125335 125337 0.656177156
## 1632 chr18 125369 125371 0.656177156
## 1633 chr18 125379 125381 0.656177156
## 1634 chr18 125383 125385 0.656177156
## 1635 chr18 125391 125393 0.174242424
## 1636 chr18 125395 125397 0.174242424
## 1637 chr18 125415 125417 0.174242424
## 1638 chr18 125439 125441 0.041666667
## 1639 chr18 125454 125456 0.041666667
## 1640 chr18 125471 125473 0.000000000
## 1641 chr18 125501 125503 0.000000000
## 1642 chr18 125630 125632 0.200000000
## 1643 chr18 125715 125717 0.650000000
## 1644 chr18 125739 125741 0.650000000
## 1645 chr18 125771 125773 0.125000000
## 1646 chr18 125791 125793 0.125000000
## 1647 chr18 125835 125837 0.125000000
## 1648 chr18 125843 125845 0.125000000
## 1649 chr18 125866 125868 0.000000000
## 1650 chr18 125924 125926 0.000000000
## 1651 chr18 126153 126155 0.000000000
## 1652 chr18 126199 126201 0.000000000
## 1653 chr18 126389 126391 0.000000000
## 1654 chr18 126531 126533 0.000000000
## 1655 chr18 126557 126559 0.000000000
## 1656 chr18 127486 127488 0.500000000
## 1657 chr18 127566 127568 0.500000000
## 1658 chr18 127740 127742 1.000000000
## 1659 chr18 127786 127788 0.000000000
## 1660 chr18 127804 127806 0.000000000
## 1661 chr18 127865 127867 0.000000000
## 1662 chr18 127991 127993 0.000000000
## 1663 chr18 128194 128196 0.000000000
## 1664 chr18 128434 128436 0.000000000
## 1665 chr18 128480 128482 0.000000000
## 1666 chr18 128845 128847 0.000000000
## 1667 chr18 128886 128888 0.000000000
## 1668 chr18 129015 129017 0.000000000
## 1669 chr18 129040 129042 0.000000000
## 1670 chr18 129175 129177 0.000000000
## 1671 chr18 129211 129213 0.000000000
## 1672 chr18 129429 129431 0.000000000
## 1673 chr18 129450 129452 0.000000000
## 1674 chr18 129659 129661 1.000000000
## 1675 chr18 129819 129821 0.500000000
## 1676 chr18 129832 129834 0.500000000
## 1677 chr18 130108 130110 0.000000000
## 1678 chr18 130228 130230 0.000000000
## 1679 chr18 130530 130532 0.000000000
## 1680 chr18 130645 130647 0.000000000
## 1681 chr18 130788 130790 0.000000000
## 1682 chr18 130920 130922 0.000000000
## 1683 chr18 130943 130945 0.000000000
## 1684 chr18 131138 131140 0.000000000
## 1685 chr18 131221 131223 1.000000000
## 1686 chr18 131264 131266 1.000000000
## 1687 chr18 131800 131802 0.000000000
## 1688 chr18 131925 131927 0.000000000
## 1689 chr18 131941 131943 0.000000000
## 1690 chr18 132001 132003 1.000000000
## 1691 chr18 132151 132153 0.000000000
## 1692 chr18 132331 132333 0.000000000
## 1693 chr18 132834 132836 0.725013291
## 1694 chr18 132842 132844 0.725013291
## 1695 chr18 132844 132846 0.725013291
## 1696 chr18 132854 132856 1.110015949
## 1697 chr18 132866 132868 1.110015949
## 1698 chr18 132887 132889 1.110015949
## 1699 chr18 132914 132916 0.282280702
## 1700 chr18 132945 132947 0.132631579
## 1701 chr18 132973 132975 0.580000000
## 1702 chr18 133009 133011 0.250000000
## 1703 chr18 133041 133043 0.250000000
## 1704 chr18 133263 133265 0.000000000
## 1705 chr18 133456 133458 0.000000000
## 1706 chr18 133869 133871 0.000000000
## 1707 chr18 133922 133924 1.000000000
## 1708 chr18 133975 133977 1.000000000
## 1709 chr18 134084 134086 0.000000000
## 1710 chr18 134296 134298 0.555555556
## 1711 chr18 134349 134351 1.844444444
## 1712 chr18 134355 134357 0.883333333
## 1713 chr18 134450 134452 1.150000000
## 1714 chr18 134472 134474 0.566666667
## 1715 chr18 134681 134683 0.000000000
## 1716 chr18 135212 135214 1.000000000
## 1717 chr18 135452 135454 0.000000000
## 1718 chr18 135516 135518 0.000000000
## 1719 chr18 135915 135917 0.000000000
## 1720 chr18 135973 135975 0.000000000
## 1721 chr18 136353 136355 0.000000000
## 1722 chr18 136458 136460 3.350000000
## 1723 chr18 136469 136471 3.350000000
## 1724 chr18 136601 136603 3.856776557
## 1725 chr18 136629 136631 0.778388278
## 1726 chr18 136670 136672 0.296703297
## 1727 chr18 136691 136693 0.296703297
## 1728 chr18 136704 136706 0.071428571
## 1729 chr18 136952 136954 0.869701941
## 1730 chr18 136956 136958 0.869701941
## 1731 chr18 136974 136976 0.869701941
## 1732 chr18 136997 136999 0.869701941
## 1733 chr18 137001 137003 0.495761553
## 1734 chr18 137031 137033 0.559431803
## 1735 chr18 137061 137063 0.953701279
## 1736 chr18 137071 137073 0.953701279
## 1737 chr18 137073 137075 0.682314706
## 1738 chr18 137094 137096 0.471633630
## 1739 chr18 137115 137117 1.269950444
## 1740 chr18 137132 137134 1.667466306
## 1741 chr18 137149 137151 2.213523281
## 1742 chr18 137155 137157 2.213523281
## 1743 chr18 137187 137189 1.040184672
## 1744 chr18 137344 137346 0.000000000
## 1745 chr18 137435 137437 0.000000000
## 1746 chr18 137500 137502 0.000000000
## 1747 chr18 137578 137580 0.000000000
## 1748 chr18 137694 137696 0.000000000
## 1749 chr18 137788 137790 0.000000000
## 1750 chr18 137828 137830 1.000000000
## 1751 chr18 137971 137973 0.333333333
## 1752 chr18 138036 138038 0.333333333
## 1753 chr18 138046 138048 0.333333333
## 1754 chr18 138213 138215 1.777777778
## 1755 chr18 138233 138235 3.222222222
## 1756 chr18 138364 138366 1.500000000
## 1757 chr18 138372 138374 1.500000000
## 1758 chr18 138780 138782 1.000000000
## 1759 chr18 138899 138901 0.000000000
## 1760 chr18 138913 138915 0.000000000
## 1761 chr18 138991 138993 0.000000000
## 1762 chr18 139301 139303 2.333333333
## 1763 chr18 139345 139347 2.333333333
## 1764 chr18 139387 139389 0.333333333
## 1765 chr18 139445 139447 0.000000000
## 1766 chr18 139678 139680 0.000000000
## 1767 chr18 139766 139768 0.000000000
## 1768 chr18 139835 139837 0.000000000
## 1769 chr18 139850 139852 1.000000000
## 1770 chr18 140054 140056 0.500000000
## 1771 chr18 140065 140067 0.500000000
## 1772 chr18 140250 140252 0.000000000
## 1773 chr18 140404 140406 0.000000000
## 1774 chr18 140433 140435 0.333333333
## 1775 chr18 140469 140471 0.333333333
## 1776 chr18 140549 140551 0.333333333
## 1777 chr18 140758 140760 0.250000000
## 1778 chr18 140865 140867 1.226470588
## 1779 chr18 140899 140901 0.619327731
## 1780 chr18 140905 140907 1.047992530
## 1781 chr18 141001 141003 3.071486928
## 1782 chr18 141009 141011 3.437500000
## 1783 chr18 141130 141132 0.347222222
## 1784 chr18 141405 141407 0.392857143
## 1785 chr18 141442 141444 0.839285714
## 1786 chr18 141446 141448 0.839285714
## 1787 chr18 141500 141502 0.309523810
## 1788 chr18 141519 141521 0.309523810
## 1789 chr18 141536 141538 0.309523810
## 1790 chr18 141612 141614 0.666666667
## 1791 chr18 141681 141683 2.333333333
## 1792 chr18 141770 141772 3.000000000
## 1793 chr18 141880 141882 0.500000000
## 1794 chr18 141935 141937 0.500000000
## 1795 chr18 142055 142057 0.000000000
## 1796 chr18 142221 142223 1.068965517
## 1797 chr18 142272 142274 0.143039591
## 1798 chr18 142281 142283 0.318007663
## 1799 chr18 142340 142342 0.842512771
## 1800 chr18 142344 142346 0.842512771
## 1801 chr18 142356 142358 1.283742598
## 1802 chr18 142366 142368 1.283742598
## 1803 chr18 142398 142400 0.569749216
## 1804 chr18 142432 142434 0.323863636
## 1805 chr18 142478 142480 0.323863636
## 1806 chr18 142585 142587 0.000000000
## 1807 chr18 142816 142818 0.000000000
## 1808 chr18 142876 142878 1.000000000
## 1809 chr18 143008 143010 0.000000000
## 1810 chr18 143209 143211 0.403846154
## 1811 chr18 143225 143227 0.625418060
## 1812 chr18 143251 143253 0.900820194
## 1813 chr18 143269 143271 0.619288663
## 1814 chr18 143297 143299 3.234537188
## 1815 chr18 143309 143311 3.234537188
## 1816 chr18 143349 143351 2.862450449
## 1817 chr18 143427 143429 1.425398535
## 1818 chr18 143437 143439 0.739739374
## 1819 chr18 143462 143464 0.483375959
## 1820 chr18 143525 143527 1.270588235
## 1821 chr18 143556 143558 0.975000000
## 1822 chr18 143564 143566 0.975000000
## 1823 chr18 143650 143652 1.250000000
## 1824 chr18 143802 143804 0.666666667
## 1825 chr18 143854 143856 0.666666667
## 1826 chr18 143874 143876 0.666666667
## 1827 chr18 144092 144094 1.300802139
## 1828 chr18 144120 144122 2.120248591
## 1829 chr18 144129 144131 2.120248591
## 1830 chr18 144139 144141 2.120248591
## 1831 chr18 144167 144169 0.589680590
## 1832 chr18 144176 144178 0.589680590
## 1833 chr18 144265 144267 1.605757576
## 1834 chr18 144275 144277 1.240000000
## 1835 chr18 144298 144300 1.240000000
## 1836 chr18 144319 144321 1.240000000
## 1837 chr18 144359 144361 0.833333333
## 1838 chr18 144418 144420 0.000000000
## 1839 chr18 144917 144919 0.000000000
## 1840 chr18 145108 145110 0.000000000
## 1841 chr18 145537 145539 0.000000000
## 1842 chr18 145546 145548 0.000000000
## 1843 chr18 145690 145692 0.000000000
## 1844 chr18 145793 145795 1.000000000
## 1845 chr18 145833 145835 1.000000000
## 1846 chr18 146361 146363 0.000000000
## 1847 chr18 146502 146504 0.500000000
## 1848 chr18 146564 146566 0.500000000
## 1849 chr18 146648 146650 0.313131313
## 1850 chr18 146718 146720 2.168350168
## 1851 chr18 146727 146729 2.168350168
## 1852 chr18 146736 146738 2.168350168
## 1853 chr18 146770 146772 1.181818182
## 1854 chr18 146885 146887 0.000000000
## 1855 chr18 146893 146895 0.000000000
## 1856 chr18 146901 146903 0.000000000
## 1857 chr18 146923 146925 0.000000000
## 1858 chr18 146925 146927 0.000000000
## 1859 chr18 146931 146933 0.000000000
## 1860 chr18 146948 146950 0.000000000
## 1861 chr18 146955 146957 0.000000000
## 1862 chr18 146963 146965 0.000000000
## 1863 chr18 146976 146978 0.000000000
## 1864 chr18 146987 146989 0.000000000
## 1865 chr18 147007 147009 0.000000000
## 1866 chr18 147011 147013 0.000000000
## 1867 chr18 147019 147021 0.000000000
## 1868 chr18 147023 147025 0.000000000
## 1869 chr18 147055 147057 1.000000000
## 1870 chr18 147066 147068 1.000000000
## 1871 chr18 147086 147088 1.000000000
## 1872 chr18 147100 147102 1.000000000
## 1873 chr18 147107 147109 1.000000000
## 1874 chr18 147111 147113 1.000000000
## 1875 chr18 147116 147118 1.000000000
## 1876 chr18 147144 147146 1.000000000
## 1877 chr18 147154 147156 1.000000000
## 1878 chr18 147160 147162 1.000000000
## 1879 chr18 147245 147247 0.000000000
## 1880 chr18 147355 147357 0.276190476
## 1881 chr18 147359 147361 0.276190476
## 1882 chr18 147361 147363 0.276190476
## 1883 chr18 147371 147373 0.276190476
## 1884 chr18 147415 147417 0.276190476
## 1885 chr18 147429 147431 0.276190476
## 1886 chr18 147449 147451 0.276190476
## 1887 chr18 147460 147462 0.066666667
## 1888 chr18 147502 147504 0.333333333
## 1889 chr18 147510 147512 0.333333333
## 1890 chr18 147534 147536 0.333333333
## 1891 chr18 147558 147560 0.333333333
## 1892 chr18 147566 147568 0.333333333
## 1893 chr18 147573 147575 0.333333333
## 1894 chr18 147596 147598 0.333333333
## 1895 chr18 147598 147600 0.333333333
## 1896 chr18 147627 147629 0.333333333
## 1897 chr18 147730 147732 0.000000000
## 1898 chr18 147768 147770 0.000000000
## 1899 chr18 147772 147774 0.000000000
## 1900 chr18 148033 148035 1.000000000
## 1901 chr18 148118 148120 1.000000000
## 1902 chr18 148465 148467 0.000000000
## 1903 chr18 148702 148704 0.500000000
## 1904 chr18 148719 148721 0.500000000
## 1905 chr18 148765 148767 0.142857143
## 1906 chr18 148773 148775 0.535714286
## 1907 chr18 148835 148837 0.535714286
## 1908 chr18 148862 148864 0.535714286
## 1909 chr18 148911 148913 0.125000000
## 1910 chr18 148920 148922 0.125000000
## 1911 chr18 149027 149029 0.000000000
## 1912 chr18 149193 149195 0.428571429
## 1913 chr18 149220 149222 0.428571429
## 1914 chr18 149255 149257 1.402597403
## 1915 chr18 149306 149308 2.837229437
## 1916 chr18 149381 149383 2.282284382
## 1917 chr18 149390 149392 2.282284382
## 1918 chr18 149408 149410 0.628205128
## 1919 chr18 149441 149443 1.128846154
## 1920 chr18 149451 149453 1.900320513
## 1921 chr18 149506 149508 0.514423077
## 1922 chr18 149589 149591 0.833333333
## 1923 chr18 149656 149658 0.333333333
## 1924 chr18 149751 149753 0.000000000
## 1925 chr18 149808 149810 1.000000000
## 1926 chr18 149966 149968 0.000000000
## 1927 chr18 150052 150054 0.000000000
## 1928 chr18 150105 150107 0.000000000
## 1929 chr18 150348 150350 0.000000000
## 1930 chr18 150384 150386 0.000000000
## 1931 chr18 150406 150408 0.000000000
## 1932 chr18 150412 150414 0.000000000
## 1933 chr18 150571 150573 0.000000000
## 1934 chr18 150604 150606 0.000000000
## 1935 chr18 150631 150633 0.000000000
## 1936 chr18 150662 150664 1.000000000
## 1937 chr18 150691 150693 1.000000000
## 1938 chr18 151049 151051 0.000000000
## 1939 chr18 151103 151105 0.000000000
## 1940 chr18 151114 151116 0.000000000
## 1941 chr18 151281 151283 2.200000000
## 1942 chr18 151318 151320 0.800000000
## 1943 chr18 151426 151428 0.000000000
## 1944 chr18 151454 151456 0.000000000
## 1945 chr18 152036 152038 3.000000000
## 1946 chr18 152398 152400 1.666666667
## 1947 chr18 152470 152472 0.333333333
## 1948 chr18 152720 152722 0.000000000
## 1949 chr18 152736 152738 0.000000000
## 1950 chr18 152744 152746 0.000000000
## 1951 chr18 152783 152785 0.000000000
## 1952 chr18 153065 153067 0.000000000
## 1953 chr18 153209 153211 1.000000000
## 1954 chr18 153295 153297 0.000000000
## 1955 chr18 153352 153354 0.000000000
## 1956 chr18 153482 153484 0.000000000
## 1957 chr18 153521 153523 0.140740741
## 1958 chr18 153545 153547 0.304861111
## 1959 chr18 153550 153552 0.304861111
## 1960 chr18 153582 153584 0.304861111
## 1961 chr18 153613 153615 0.580394525
## 1962 chr18 153636 153638 0.580394525
## 1963 chr18 153640 153642 0.580394525
## 1964 chr18 153645 153647 0.580394525
## 1965 chr18 153661 153663 0.324184783
## 1966 chr18 153683 153685 0.149456522
## 1967 chr18 153689 153691 0.149456522
## 1968 chr18 153791 153793 0.062500000
## 1969 chr18 153875 153877 1.247282609
## 1970 chr18 153887 153889 1.247282609
## 1971 chr18 153891 153893 1.247282609
## 1972 chr18 153951 153953 1.559782609
## 1973 chr18 153979 153981 0.635869565
## 1974 chr18 154304 154306 0.000000000
## 1975 chr18 154357 154359 1.300000000
## 1976 chr18 154365 154367 1.300000000
## 1977 chr18 154484 154486 0.981818182
## 1978 chr18 154522 154524 0.792344498
## 1979 chr18 154527 154529 0.792344498
## 1980 chr18 154536 154538 0.792344498
## 1981 chr18 154554 154556 0.792344498
## 1982 chr18 154616 154618 0.196172249
## 1983 chr18 154626 154628 0.052631579
## 1984 chr18 154670 154672 0.500000000
## 1985 chr18 154687 154689 0.500000000
## 1986 chr18 154882 154884 1.000000000
## 1987 chr18 155278 155280 0.444444444
## 1988 chr18 155287 155289 1.000000000
## 1989 chr18 155308 155310 2.000000000
## 1990 chr18 155413 155415 0.555555556
## 1991 chr18 155565 155567 0.000000000
## 1992 chr18 155576 155578 0.000000000
## 1993 chr18 155660 155662 0.000000000
## 1994 chr18 155676 155678 0.000000000
## 1995 chr18 155704 155706 0.000000000
## 1996 chr18 155797 155799 0.000000000
## 1997 chr18 155847 155849 0.000000000
## 1998 chr18 155868 155870 0.000000000
## 1999 chr18 155915 155917 0.000000000
## 2000 chr18 155969 155971 0.000000000In order to detect different methylated CpG sites, we should calculate p-value of each site. The below codes are calculate p-value of each site with function EMtest(). The input files which include “datafile”, “cpgfile” and “mrecpgfile” are should have been generated by Step 1. The output file “writefile” will owneleven columns, that is, “chr”, “chrSt”,“chrEnd”, “Medip1”,“Medip2”, “MRE1”, “MRE2”, “cg”,“mrecg”,“pvalue”,“Ts”. We also output a reportfile which will include parameters “s1/s2”; “s3/s4”; “N1”; “N2”; “N3”; “N4”; “c1”; “c2” and “Spend time”.
data(example_data)
data1 <- EM2_H1ESB1_MeDIP_sigleCpG
data2 <- EM2_H1ESB2_MeDIP_sigleCpG
data3 <- H1ESB1_MRE_sigleCpG
data4 <- H1ESB2_MRE_sigleCpG
datafile <- cbind(data1,data2,data3,data4)
allcpg <- all_CpGsite_bin_chr18
mrecpg <- three_mre_cpg
dirwrite <-paste(setwd(getwd()), "/", sep="")
writefile <- paste(dirwrite, "pval_EM_H1ESB1_H1ESB21.bed", sep="")
reportfile <- paste(dirwrite, "report_pvalH1ESB1_H1ESB21.bed", sep="")
EMtest(datafile=datafile, chrstring=NULL, cpgfile=allcpg,mrecpgfile=mrecpg,
writefile=writefile, reportfile=reportfile,mreratio=3/7, psd=2,
mkadded=1, f=1)## reading data ....## adjustment weight f is :## [1] 1## Top line of dataset:## V1 V2 V3 V4 data2[, 4] data3[, 4] data4[, 4]
## 1 chr18 10692 10694 8.824992 7.185892 0 0
## V1 V2 V3 V4
## 1 chr18 10692 10694 1
## V1 V2 V3 V4
## 1 chr18 10692 10694 0## Computing p-values for only MeDIP-seq windows: 1286## Computing p-values for MeDIP-seq
## and MRE-seq windows: 714## Exact compute p-values with product binomial distribution.## Output to writefile.## The End.After getting p-values, we choose differentially expressed methylated CpG sites with p-values. The input file is the file which have been generated by Step 2. Then we assume the sites to be differentially expressed methylated CpGs when p-values less than pre-setting cutoffs, such as \(10^{-3}\) or \(10^{-5}\).