OAKL to the Browser

Working in Rmd, here is getting some DMLs into IGV format. TLDR - bedfile


Methylkit-02

Now I need to download the files

curl -O http://owl.fish.washington.edu/halfshell/bu-serine-wd/18-04-29/zr2096_[1-10]_dedup.sorted.bam

These were generated in Jupyter like:

%%bash
find /Volumes/Serine/wd/18-04-27/zr2096_*R1* \
| xargs basename -s _s1_R1_val_1.fq.gz | xargs -I{} /Applications/bioinfo/Bismark_v0.19.0/bismark \
--path_to_bowtie /Applications/bioinfo/bowtie2-2.3.4.1-macos-x86_64 \
--genome /Volumes/Serine/wd/18-03-15/genome \
--score_min L,0,-1.2 \
-p 4 \
--non_directional \
-1 /Volumes/Serine/wd/18-04-27/{}_s1_R1_val_1.fq.gz \
-2 /Volumes/Serine/wd/18-04-27/{}_s1_R2_val_2.fq.gz \
2> bismark.err

%%bash
/Applications/bioinfo/Bismark_v0.19.0/deduplicate_bismark \
--bam -p \
*.bam \
2> dedup.err

%%bash
find *deduplicated.bam \
| xargs basename -s _s1_R1_val_1_bismark_bt2_pe.deduplicated.bam | xargs -I{} /Applications/bioinfo/samtools-1.3.1/samtools \
sort {}_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam -o {}_dedup.sorted.bam

Reading in some files:

file.list=list(  '/Users/sr320/Desktop/oakl/zr2096_1_dedup.sorted.bam',
                 '/Users/sr320/Desktop/oakl/zr2096_2_dedup.sorted.bam',
                 '/Users/sr320/Desktop/oakl/zr2096_3_dedup.sorted.bam',
                 '/Users/sr320/Desktop/oakl/zr2096_4_dedup.sorted.bam',
                 '/Users/sr320/Desktop/oakl/zr2096_5_dedup.sorted.bam',
                 '/Users/sr320/Desktop/oakl/zr2096_6_dedup.sorted.bam',
                 '/Users/sr320/Desktop/oakl/zr2096_7_dedup.sorted.bam',
                 '/Users/sr320/Desktop/oakl/zr2096_8_dedup.sorted.bam',
                 '/Users/sr320/Desktop/oakl/zr2096_9_dedup.sorted.bam',
                 '/Users/sr320/Desktop/oakl/zr2096_10_dedup.sorted.bam'
)

Bringing in bam files, setting context, AND coverage

myobj = processBismarkAln(location = file.list, sample.id = list("1","2","3","4","5","6","7","8","9","10"), assembly = "v3", read.context="CpG", mincov=10, treatment = c(0,0,0,0,0,1,1,1,1,1))
save(myobj, file = "../analyses/myobj_180427files")
load("../analyses/myobj_180427files")
getCoverageStats(myobj[[4]],plot=TRUE,both.strands=FALSE)

getMethylationStats(myobj[[1]],plot=FALSE,both.strands=FALSE)
## methylation statistics per base
## summary:
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
##    0.00   83.33   93.33   85.11  100.00  100.00
## percentiles:
##        0%       10%       20%       30%       40%       50%       60%
##   0.00000  55.55556  80.00000  85.71429  90.47619  93.33333  96.29630
##       70%       80%       90%       95%       99%     99.5%     99.9%
## 100.00000 100.00000 100.00000 100.00000 100.00000 100.00000 100.00000
##      100%
## 100.00000
getCoverageStats(myobj[[4]],plot=TRUE,both.strands=FALSE)

meth=unite(myobj)
getCorrelation(meth,plot=TRUE)
##            1         2         3         4         5         6         7
## 1  1.0000000 0.4486002 0.4560082 0.4404980 0.4331196 0.4820232 0.4782540
## 2  0.4486002 1.0000000 0.5205769 0.5071152 0.4994732 0.4561182 0.5355796
## 3  0.4560082 0.5205769 1.0000000 0.5078281 0.5042024 0.4610765 0.5485566
## 4  0.4404980 0.5071152 0.5078281 1.0000000 0.4999247 0.4532686 0.5325240
## 5  0.4331196 0.4994732 0.5042024 0.4999247 1.0000000 0.4484705 0.5300285
## 6  0.4820232 0.4561182 0.4610765 0.4532686 0.4484705 1.0000000 0.5713013
## 7  0.4782540 0.5355796 0.5485566 0.5325240 0.5300285 0.5713013 1.0000000
## 8  0.4427913 0.5140576 0.5175793 0.5032337 0.4955144 0.4546524 0.5355500
## 9  0.4579275 0.5216281 0.5311598 0.5135430 0.5025602 0.4660443 0.5469018
## 10 0.4309082 0.5077382 0.5148965 0.5017601 0.4975297 0.4342481 0.5280633
##            8         9        10
## 1  0.4427913 0.4579275 0.4309082
## 2  0.5140576 0.5216281 0.5077382
## 3  0.5175793 0.5311598 0.5148965
## 4  0.5032337 0.5135430 0.5017601
## 5  0.4955144 0.5025602 0.4975297
## 6  0.4546524 0.4660443 0.4342481
## 7  0.5355500 0.5469018 0.5280633
## 8  1.0000000 0.5192701 0.4981650
## 9  0.5192701 1.0000000 0.5222376
## 10 0.4981650 0.5222376 1.0000000

clusterSamples(meth, dist="correlation", method="ward", plot=TRUE)
## The "ward" method has been renamed to "ward.D"; note new "ward.D2"

##
## Call:
## hclust(d = d, method = HCLUST.METHODS[hclust.method])
##
## Cluster method   : ward.D
## Distance         : pearson
## Number of objects: 10
PCASamples(meth, screeplot=TRUE)

myDiff=calculateDiffMeth(meth)
## two groups detected:
##  will calculate methylation difference as the difference of
## treatment (group: 1) - control (group: 0)
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred

## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred

## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## Warning: glm.fit: algorithm did not converge
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
myDiff50p=getMethylDiff(myDiff,difference=50,qvalue=0.01)
myDiff50p
##                chr     start       end strand        pvalue        qvalue
## 677    NC_035780.1    346073    346073      -  2.658918e-24  3.403025e-22
## 2364   NC_035780.1    990997    990997      -  2.731237e-29  5.781425e-27
## 2834   NC_035780.1   1959000   1959000      -  3.962712e-85  3.474108e-81
## 3329   NC_035780.1   2541728   2541728      -  1.177599e-26  1.908906e-24
## 3698   NC_035780.1   2584493   2584493      +  6.347756e-56  1.165188e-52
## 3727   NC_035780.1   2586510   2586510      -  1.060224e-35  3.983563e-33
## 3739   NC_035780.1   2588795   2588795      +  1.412833e-74  7.250515e-71
## 3740   NC_035780.1   2588796   2588796      -  2.118407e-43  1.553064e-40
## 3750   NC_035780.1   2589722   2589722      -  2.915792e-14  1.093788e-12
## 4576   NC_035780.1   4286287   4286287      +  1.761183e-82  1.277817e-78
## 4585   NC_035780.1   4288214   4288214      +  2.525530e-25  3.563994e-23
## 7788   NC_035780.1  15389759  15389759      -  1.340609e-25  1.944002e-23
## 8149   NC_035780.1  15534532  15534532      +  1.422063e-56  2.849650e-53
## 9283   NC_035780.1  17500582  17500582      +  2.234699e-57  4.609786e-54
## 10727  NC_035780.1  19482570  19482570      -  1.500898e-53  2.288412e-50
## 13384  NC_035780.1  21941412  21941412      -  6.151680e-77  3.498276e-73
## 14277  NC_035780.1  23288707  23288707      +  1.036531e-25  1.519820e-23
## 15236  NC_035780.1  24245856  24245856      -  5.945674e-30  1.340854e-27
## 16189  NC_035780.1  25201661  25201661      -  5.673392e-36  2.198391e-33
## 16404  NC_035780.1  25437703  25437703      +  1.537943e-41  9.746847e-39
## 16504  NC_035780.1  25858299  25858299      -  1.189348e-26  1.924986e-24
## 18541  NC_035780.1  26637856  26637856      -  1.110870e-64  3.710091e-61
## 19466  NC_035780.1  27396184  27396184      -  4.156354e-28  7.871555e-26
## 20393  NC_035780.1  28493521  28493521      -  1.023069e-27  1.849329e-25
## 20625  NC_035780.1  28739458  28739458      +  4.339304e-48  4.207483e-45
## 20629  NC_035780.1  28739473  28739473      +  3.458688e-59  7.825109e-56
## 20630  NC_035780.1  28739474  28739474      -  8.600582e-50  9.781785e-47
## 22477  NC_035780.1  31303160  31303160      +  9.360813e-28  1.699386e-25
## 22482  NC_035780.1  31303208  31303208      +  8.217262e-42  5.352869e-39
## 23488  NC_035780.1  32447268  32447268      +  1.315527e-27  2.342168e-25
## 23680  NC_035780.1  32698174  32698174      +  4.772501e-28  8.973831e-26
## 23757  NC_035780.1  32704774  32704774      +  6.079553e-18  3.751278e-16
## 23794  NC_035780.1  32717031  32717031      +  4.910371e-28  9.224828e-26
## 23935  NC_035780.1  32781382  32781382      +  4.725453e-33  1.396450e-30
## 23936  NC_035780.1  32781383  32781383      -  4.396936e-27  7.448873e-25
## 24023  NC_035780.1  32787978  32787978      -  1.104950e-40  6.567518e-38
## 24580  NC_035780.1  33209728  33209728      -  1.496176e-22  1.558451e-20
## 26267  NC_035780.1  38085932  38085932      +  7.664890e-25  1.032492e-22
## 26769  NC_035780.1  39872842  39872842      +  4.816855e-55  8.173421e-52
## 26770  NC_035780.1  39872843  39872843      -  2.473306e-31  6.315572e-29
## 26841  NC_035780.1  39890298  39890298      +  5.830127e-27  9.751229e-25
## 30905  NC_035780.1  48579390  48579390      -  2.042457e-42  1.390774e-39
## 31771  NC_035780.1  54211053  54211053      +  3.156324e-34  1.034448e-31
## 31772  NC_035780.1  54211054  54211054      -  1.833263e-32  5.082121e-30
## 32478  NC_035780.1  55378083  55378083      +  2.398040e-21  2.189009e-19
## 34197  NC_035780.1  58135769  58135769      -  3.547089e-37  1.548414e-34
## 35498  NC_035780.1  60359487  60359487      +  5.479159e-87  5.012427e-83
## 35499  NC_035780.1  60359488  60359488      -  5.705224e-54  9.094122e-51
## 36337  NC_035780.1  61420662  61420662      -  3.078850e-19  2.199709e-17
## 36931  NC_035780.1  62750218  62750218      +  4.618934e-37  2.003835e-34
## 37651  NC_035780.1  63619402  63619402      +  1.922326e-35  7.046558e-33
## 39044  NC_035781.1    627421    627421      +  5.652169e-25  7.737546e-23
## 39153  NC_035781.1    631900    631900      +  1.703347e-20  1.413797e-18
## 39154  NC_035781.1    631901    631901      -  2.376178e-28  4.603743e-26
## 40929  NC_035781.1   1680603   1680603      +  4.020120e-23  4.520924e-21
## 41205  NC_035781.1   2277405   2277405      +  1.283425e-57  2.727704e-54
## 43115  NC_035781.1   3401690   3401690      -  6.930542e-45  5.544641e-42
## 46173  NC_035781.1   5648773   5648773      -  3.565842e-64  1.154279e-60
## 46593  NC_035781.1   5855169   5855169      -  1.866491e-63  5.861558e-60
## 48703  NC_035781.1   9369564   9369564      +  3.682392e-27  6.258515e-25
## 49787  NC_035781.1  10383012  10383012      -  7.984320e-37  3.393866e-34
## 49838  NC_035781.1  10426303  10426303      + 2.064579e-115 5.212371e-111
## 49862  NC_035781.1  10427420  10427420      +  7.264465e-53  1.032771e-49
## 49871  NC_035781.1  10427643  10427643      +  5.208414e-56  9.872895e-53
## 50894  NC_035781.1  11919273  11919273      +  7.975521e-22  7.673125e-20
## 50940  NC_035781.1  11960874  11960874      -  3.324978e-68  1.371768e-64
## 51560  NC_035781.1  13033012  13033012      -  8.565343e-53  1.201477e-49
## 52473  NC_035781.1  13841609  13841609      +  1.047258e-41  6.697610e-39
## 53501  NC_035781.1  15604575  15604575      +  1.379211e-66  5.091172e-63
## 54080  NC_035781.1  19453326  19453326      -  1.502676e-26  2.398899e-24
## 55540  NC_035781.1  20620125  20620125      -  1.024992e-24  1.359813e-22
## 57179  NC_035781.1  22901074  22901074      -  2.559524e-47  2.393529e-44
## 57545  NC_035781.1  23710327  23710327      +  4.724519e-24  5.892567e-22
## 57573  NC_035781.1  24047932  24047932      -  2.017265e-19  1.474804e-17
## 58598  NC_035781.1  26609798  26609798      -  2.927812e-61  7.700433e-58
## 59827  NC_035781.1  29401028  29401028      +  1.898658e-18  1.241817e-16
## 60837  NC_035781.1  29991127  29991127      -  3.582980e-40  2.010366e-37
## 61103  NC_035781.1  30153251  30153251      +  4.568087e-43  3.269257e-40
## 61104  NC_035781.1  30153252  30153252      -  5.459769e-96  7.658523e-92
## 61747  NC_035781.1  30488985  30488985      +  1.837270e-41  1.153958e-38
## 63331  NC_035781.1  32146060  32146060      +  1.130574e-34  3.899700e-32
## 66631  NC_035781.1  40747578  40747578      +  6.560384e-40  3.576053e-37
## 68399  NC_035781.1  42529449  42529449      +  3.953855e-21  3.525094e-19
## 68646  NC_035781.1  43054124  43054124      -  4.576343e-25  6.318232e-23
## 68979  NC_035781.1  45110045  45110045      -  1.786608e-54  2.959971e-51
## 68984  NC_035781.1  45110114  45110114      -  2.410425e-91  3.169827e-87
## 68985  NC_035781.1  45110121  45110121      -  3.101970e-76  1.717576e-72
## 70629  NC_035781.1  52592743  52592743      +  1.226566e-35  4.592157e-33
## 70630  NC_035781.1  52592744  52592744      - 6.766249e-118 2.033817e-113
## 70636  NC_035781.1  52592761  52592761      -  1.242581e-79  8.170278e-76
## 71869  NC_035781.1  52956462  52956462      +  1.855078e-68  8.131731e-65
## 72147  NC_035781.1  53358701  53358701      -  7.385927e-36  2.825558e-33
## 72149  NC_035781.1  53358850  53358850      -  1.011204e-22  1.076202e-20
## 72164  NC_035781.1  53361156  53361156      +  2.396023e-26  3.745484e-24
## 72175  NC_035781.1  53364502  53364502      +  3.275649e-21  2.941623e-19
## 72176  NC_035781.1  53364503  53364503      -  7.071914e-36  2.715304e-33
## 72184  NC_035781.1  53364617  53364617      +  1.514379e-29  3.278161e-27
## 72211  NC_035781.1  53371081  53371081      +  6.364924e-17  3.447579e-15
## 72263  NC_035781.1  53385564  53385564      -  6.513187e-29  1.329220e-26
## 74940  NC_035781.1  54799287  54799287      +  6.125355e-50  7.120569e-47
## 74941  NC_035781.1  54799288  54799288      -  2.192895e-39  1.142085e-36
## 75217  NC_035781.1  56296257  56296257      +  8.271508e-24  1.003685e-21
## 75260  NC_035781.1  56595192  56595192      +  8.150144e-21  6.985151e-19
## 76886  NC_035781.1  59274790  59274790      -  2.521672e-33  7.590554e-31
## 76890  NC_035781.1  59274912  59274912      +  3.648696e-36  1.445790e-33
## 77258  NC_035781.1  59602904  59602904      - 1.586418e-107 3.034499e-103
## 77262  NC_035781.1  59604047  59604047      -  1.568595e-36  6.509758e-34
## 77438  NC_035781.1  59696863  59696863      +  2.808784e-25  3.939935e-23
## 77450  NC_035781.1  59697601  59697601      -  6.188878e-21  5.389854e-19
## 77529  NC_035781.1  59716718  59716718      +  1.484761e-44  1.152788e-41
## 77536  NC_035781.1  59717178  59717178      +  8.296425e-49  8.641748e-46
## 79111  NC_035782.1   6260448   6260448      +  5.622319e-31  1.390106e-28
## 79276  NC_035782.1   6686536   6686536      +  3.641807e-42  2.424889e-39
## 79294  NC_035782.1   6690565   6690565      +  2.867549e-87  2.873119e-83
## 80140  NC_035782.1   6897408   6897408      -  7.098967e-25  9.593312e-23
## 80589  NC_035782.1   8707638   8707638      +  1.610468e-35  5.976282e-33
## 81906  NC_035782.1  12237055  12237055      -  5.630672e-19  3.903584e-17
## 82324  NC_035782.1  13869669  13869669      +  2.643766e-45  2.207417e-42
## 82326  NC_035782.1  13869680  13869680      +  2.121359e-48  2.125479e-45
## 82841  NC_035782.1  15148527  15148527      +  5.637013e-19  3.906693e-17
## 84948  NC_035782.1  20856835  20856835      -  2.160229e-35  7.891134e-33
## 88238  NC_035782.1  22559285  22559285      -  6.667144e-49  7.018221e-46
## 88761  NC_035782.1  22960248  22960248      -  3.746399e-30  8.633865e-28
## 90375  NC_035782.1  25062577  25062577      +  3.412038e-18  2.163060e-16
## 90544  NC_035782.1  26645486  26645486      +  1.332142e-21  1.249079e-19
## 91288  NC_035782.1  29947819  29947819      +  2.306597e-20  1.886960e-18
## 92246  NC_035782.1  33020492  33020492      -  1.282104e-35  4.783063e-33
## 94627  NC_035782.1  34498894  34498894      +  1.637500e-29  3.526540e-27
## 94628  NC_035782.1  34498896  34498896      +  2.990900e-44  2.296748e-41
## 97327  NC_035782.1  37370862  37370862      -  3.470606e-57  7.089737e-54
## 97329  NC_035782.1  37370874  37370874      -  2.410235e-40  1.385608e-37
## 97366  NC_035782.1  37843187  37843187      -  4.262797e-40  2.360332e-37
## 98965  NC_035782.1  41156867  41156867      -  3.696514e-20  2.950590e-18
## 99253  NC_035782.1  41847825  41847825      -  3.847490e-36  1.515997e-33
## 99880  NC_035782.1  45857197  45857197      -  5.906739e-24  7.285020e-22
## 100040 NC_035782.1  46212750  46212750      -  9.557692e-35  3.313037e-32
## 100221 NC_035782.1  46475862  46475862      +  3.177230e-30  7.403258e-28
## 102518 NC_035782.1  49575758  49575758      -  6.338053e-28  1.172890e-25
## 103541 NC_035782.1  50620242  50620242      -  1.393761e-20  1.166501e-18
## 104280 NC_035782.1  51594720  51594720      -  1.711929e-48  1.748560e-45
## 106247 NC_035782.1  53681703  53681703      + 4.737861e-108 9.968833e-104
## 106248 NC_035782.1  53681704  53681704      -  4.781056e-47  4.336085e-44
## 108941 NC_035782.1  57058466  57058466      -  1.399815e-19  1.042592e-17
## 109796 NC_035782.1  58675270  58675270      +  1.016514e-32  2.894216e-30
## 110187 NC_035782.1  58948372  58948372      -  3.093130e-33  9.231473e-31
## 113079 NC_035782.1  63514945  63514945      +  6.490132e-52  8.534844e-49
## 114149 NC_035782.1  64758096  64758096      +  1.693195e-35  6.261189e-33
## 114150 NC_035782.1  64758097  64758097      -  1.201373e-27  2.154974e-25
## 114364 NC_035782.1  64881415  64881415      +  6.654709e-34  2.121520e-31
## 121016 NC_035783.1   2891929   2891929      +  8.540456e-22  8.190425e-20
## 121236 NC_035783.1   4336101   4336101      +  2.393075e-25  3.381611e-23
## 121844 NC_035783.1   6430848   6430848      +  9.449201e-42  6.080080e-39
## 123743 NC_035783.1  10907089  10907089      +  3.012784e-91  3.728903e-87
## 127415 NC_035783.1  15005745  15005745      -  6.935163e-65  2.392152e-61
## 128000 NC_035783.1  16217948  16217948      -  3.856933e-21  3.443059e-19
## 128301 NC_035783.1  16810366  16810366      +  3.914332e-45  3.179947e-42
## 130596 NC_035783.1  18125850  18125850      +  1.602881e-62  4.750125e-59
## 130873 NC_035783.1  18412976  18412976      +  8.593488e-20  6.589423e-18
## 132517 NC_035783.1  19526094  19526094      -  2.176185e-39  1.139021e-36
## 132784 NC_035783.1  19556698  19556698      -  4.891592e-34  1.583430e-31
## 136680 NC_035783.1  20719352  20719352      +  2.947383e-34  9.720259e-32
## 136932 NC_035783.1  20753581  20753581      -  2.050854e-24  2.640855e-22
## 137735 NC_035783.1  20844475  20844475      +  6.690171e-50  7.650351e-47
## 137887 NC_035783.1  20856442  20856442      -  7.220329e-36  2.767239e-33
## 138382 NC_035783.1  20908985  20908985      -  1.372066e-47  1.306305e-44
## 138580 NC_035783.1  20953373  20953373      + 2.408166e-126 8.444951e-122
## 138581 NC_035783.1  20953374  20953374      -  1.749637e-48  1.778441e-45
## 138643 NC_035783.1  20963956  20963956      +  1.540060e-17  9.013650e-16
## 138940 NC_035783.1  21066969  21066969      +  1.593623e-71  7.451350e-68
## 138941 NC_035783.1  21066970  21066970      -  4.763548e-41  2.905183e-38
## 138942 NC_035783.1  21066995  21066995      +  2.403478e-97  3.612219e-93
## 138943 NC_035783.1  21066996  21066996      -  3.185999e-49  3.491455e-46
## 139015 NC_035783.1  21071070  21071070      +  3.044965e-62  8.657900e-59
## 139086 NC_035783.1  21073268  21073268      -  1.368385e-48  1.404483e-45
## 139127 NC_035783.1  21076422  21076422      -  3.299692e-29  6.908271e-27
## 139136 NC_035783.1  21076507  21076507      +  1.996555e-60  4.884779e-57
## 139178 NC_035783.1  21109546  21109546      +  1.068105e-36  4.494753e-34
## 139695 NC_035783.1  23527093  23527093      +  3.180550e-45  2.614112e-42
## 140002 NC_035783.1  23693497  23693497      +  3.430496e-28  6.567821e-26
## 140110 NC_035783.1  23889432  23889432      +  4.252729e-42  2.813861e-39
## 140219 NC_035783.1  23921625  23921625      +  1.183910e-16  6.146164e-15
## 141159 NC_035783.1  25301968  25301968      +  1.325489e-32  3.753611e-30
## 141200 NC_035783.1  25307879  25307879      +  5.345963e-50  6.249070e-47
## 142465 NC_035783.1  30742309  30742309      -  2.203892e-26  3.452838e-24
## 142908 NC_035783.1  32082627  32082627      +  1.558239e-33  4.800377e-31
## 142963 NC_035783.1  32197766  32197766      -  2.268598e-17  1.299567e-15
## 143044 NC_035783.1  32417240  32417240      -  9.712676e-43  6.812078e-40
## 146511 NC_035783.1  36586661  36586661      -  1.712352e-14  6.647462e-13
## 146977 NC_035783.1  37764810  37764810      +  2.263164e-15  9.869170e-14
## 147327 NC_035783.1  42295608  42295608      +  4.654966e-52  6.238481e-49
## 148457 NC_035783.1  45068803  45068803      +  6.413415e-32  1.714655e-29
## 148458 NC_035783.1  45068804  45068804      -  4.381474e-19  3.068897e-17
## 148988 NC_035783.1  45436572  45436572      -  2.233416e-65  7.832139e-62
## 150110 NC_035783.1  46125340  46125340      -  8.328756e-35  2.906195e-32
## 150654 NC_035783.1  47273230  47273230      +  4.372906e-18  2.736745e-16
## 150655 NC_035783.1  47273231  47273231      -  8.777753e-45  6.891449e-42
## 151588 NC_035783.1  48434287  48434287      +  2.117680e-22  2.162993e-20
## 156696 NC_035783.1  57927980  57927980      -  3.081026e-34  1.012925e-31
## 156816 NC_035783.1  58186425  58186425      -  2.894066e-34  9.559406e-32
## 156882 NC_035783.1  58980062  58980062      -  9.408058e-43  6.620500e-40
## 157293 NC_035784.1   1005579   1005579      -  1.156008e-72  5.581151e-69
## 157505 NC_035784.1   1046256   1046256      +  6.536964e-32  1.745468e-29
## 158415 NC_035784.1   1992225   1992225      -  3.822030e-24  4.815480e-22
## 158681 NC_035784.1   2011998   2011998      +  1.845194e-59  4.305612e-56
## 158710 NC_035784.1   2015412   2015412      -  1.740695e-37  7.759660e-35
## 159095 NC_035784.1   2288951   2288951      +  4.221732e-38  2.014253e-35
## 159325 NC_035784.1   2338125   2338125      -  8.594023e-23  9.235190e-21
## 159355 NC_035784.1   2340024   2340024      +  8.866231e-40  4.783397e-37
## 159439 NC_035784.1   2348439   2348439      +  8.857200e-51  1.083503e-47
## 159485 NC_035784.1   2350203   2350203      -  7.342595e-38  3.373231e-35
## 159695 NC_035784.1   2443681   2443681      -  5.171748e-36  2.011417e-33
## 159959 NC_035784.1   2777423   2777423      +  5.327754e-56  1.000894e-52
## 160330 NC_035784.1   3214006   3214006      +  1.580294e-57  3.325063e-54
## 161194 NC_035784.1   3912437   3912437      -  7.102157e-78  4.150972e-74
## 162080 NC_035784.1   7656221   7656221      +  1.975821e-34  6.641028e-32
## 162626 NC_035784.1   8045506   8045506      +  1.302983e-16  6.724502e-15
## 164573 NC_035784.1  10016146  10016146      -  2.569318e-38  1.251400e-35
## 166794 NC_035784.1  13485221  13485221      +  2.674035e-36  1.077850e-33
## 168963 NC_035784.1  19648288  19648288      -  8.751045e-29  1.767072e-26
## 170678 NC_035784.1  27176372  27176372      +  3.870284e-55  6.674904e-52
## 172233 NC_035784.1  32778721  32778721      -  1.955748e-18  1.275984e-16
## 172428 NC_035784.1  34072925  34072925      -  1.619585e-30  3.846202e-28
## 173841 NC_035784.1  36650542  36650542      -  4.080723e-28  7.756245e-26
## 174140 NC_035784.1  36797030  36797030      +  6.963609e-29  1.417019e-26
## 174141 NC_035784.1  36797031  36797031      -  2.198666e-30  5.186286e-28
## 176356 NC_035784.1  38226016  38226016      +  1.008509e-41  6.469461e-39
## 178861 NC_035784.1  42036909  42036909      +  2.669766e-56  5.201294e-53
## 179311 NC_035784.1  43356402  43356402      -  9.449414e-25  1.259969e-22
## 182037 NC_035784.1  45667414  45667414      -  1.562080e-19  1.157710e-17
## 183909 NC_035784.1  47479565  47479565      +  3.297789e-21  2.960243e-19
## 186158 NC_035784.1  50724129  50724129      -  1.030808e-19  7.815860e-18
## 187151 NC_035784.1  52291765  52291765      - 8.234357e-201 1.732574e-195
## 187153 NC_035784.1  52291781  52291781      - 6.102143e-148 6.419695e-143
## 187245 NC_035784.1  52581120  52581120      +  1.460138e-21  1.363019e-19
## 187246 NC_035784.1  52581121  52581121      -  5.937973e-54  9.393957e-51
## 187266 NC_035784.1  52581363  52581363      +  7.967674e-66  2.841460e-62
## 187267 NC_035784.1  52581364  52581364      -  2.309376e-33  7.001597e-31
## 189739 NC_035784.1  53282858  53282858      +  4.418814e-56  8.529846e-53
## 190488 NC_035784.1  53515950  53515950      +  4.932795e-15  2.065470e-13
## 191247 NC_035784.1  53991052  53991052      +  2.423737e-20  1.978942e-18
## 191514 NC_035784.1  54028110  54028110      -  2.326770e-27  4.019464e-25
## 192152 NC_035784.1  54639923  54639923      +  2.301229e-27  3.978609e-25
## 192153 NC_035784.1  54639924  54639924      -  1.301027e-39  6.965554e-37
## 193010 NC_035784.1  55154350  55154350      +  1.145187e-35  4.295122e-33
## 193012 NC_035784.1  55154408  55154408      +  9.472545e-36  3.578273e-33
## 193890 NC_035784.1  57133704  57133704      +  5.700427e-36  2.204807e-33
## 194523 NC_035784.1  57514694  57514694      -  1.661322e-39  8.804916e-37
## 194525 NC_035784.1  57514701  57514701      -  7.577121e-31  1.849520e-28
## 194734 NC_035784.1  57785891  57785891      -  2.224820e-52  3.020127e-49
## 195142 NC_035784.1  58128163  58128163      -  1.667867e-31  4.300642e-29
## 195180 NC_035784.1  58132916  58132916      +  8.116431e-20  6.237257e-18
## 195917 NC_035784.1  58834474  58834474      +  1.529437e-45  1.297604e-42
## 196178 NC_035784.1  59002732  59002732      +  9.217458e-25  1.230600e-22
## 196229 NC_035784.1  59129087  59129087      +  3.184537e-73  1.595361e-69
## 196810 NC_035784.1  59679679  59679679      +  1.972460e-29  4.221985e-27
## 196811 NC_035784.1  59679680  59679680      -  7.747376e-33  2.242241e-30
## 197684 NC_035784.1  59987571  59987571      +  1.181676e-26  1.914041e-24
## 198015 NC_035784.1  60435135  60435135      +  4.903480e-41  2.981881e-38
## 198053 NC_035784.1  60466859  60466859      +  1.009322e-18  6.797993e-17
## 198542 NC_035784.1  60893577  60893577      -  3.948002e-35  1.412739e-32
## 198670 NC_035784.1  61208184  61208184      +  2.420015e-32  6.656080e-30
## 200203 NC_035784.1  63839519  63839519      -  3.993501e-20  3.172005e-18
## 206634 NC_035784.1  67943442  67943442      +  4.288310e-31  1.072883e-28
## 206694 NC_035784.1  67991199  67991199      +  8.099492e-88  8.520985e-84
## 206695 NC_035784.1  67991200  67991200      -  7.629984e-58  1.655060e-54
## 207194 NC_035784.1  68855036  68855036      -  5.501875e-49  5.936604e-46
## 210454 NC_035784.1  74882674  74882674      +  6.652765e-24  8.143073e-22
## 212585 NC_035784.1  79434488  79434488      +  1.223315e-24  1.612946e-22
## 212590 NC_035784.1  79434840  79434840      -  4.927058e-52  6.561340e-49
## 212722 NC_035784.1  79536518  79536518      -  2.919664e-33  8.751001e-31
## 213122 NC_035784.1  79841168  79841168      -  2.972420e-33  8.883816e-31
## 213126 NC_035784.1  79841227  79841227      +  8.679293e-35  3.023496e-32
## 213127 NC_035784.1  79841228  79841228      -  6.332794e-67  2.379410e-63
## 213328 NC_035784.1  80205206  80205206      -  1.202680e-25  1.753662e-23
## 214512 NC_035784.1  82092370  82092370      +  2.140598e-23  2.491143e-21
## 215424 NC_035784.1  83406913  83406913      -  1.846599e-35  6.796522e-33
## 215966 NC_035784.1  84939270  84939270      +  9.236344e-39  4.649281e-36
## 215973 NC_035784.1  84951458  84951458      +  6.614667e-29  1.348622e-26
## 218093 NC_035784.1  87733520  87733520      +  1.376148e-84  1.072416e-80
## 218313 NC_035784.1  87914757  87914757      +  5.254276e-15  2.193453e-13
## 218712 NC_035784.1  88794181  88794181      -  2.209394e-51  2.834597e-48
## 219310 NC_035784.1  90135107  90135107      -  4.689294e-22  4.612737e-20
## 219311 NC_035784.1  90135112  90135112      -  8.244597e-27  1.359505e-24
## 219617 NC_035784.1  90817977  90817977      +  5.088677e-43  3.617222e-40
## 219795 NC_035784.1  90909623  90909623      +  3.952059e-39  2.023222e-36
## 219796 NC_035784.1  90909624  90909624      -  9.637655e-40  5.186288e-37
## 220702 NC_035784.1  93022601  93022601      -  1.446688e-19  1.075219e-17
## 222930 NC_035784.1  95099423  95099423      +  7.351917e-22  7.095877e-20
## 223008 NC_035784.1  96023006  96023006      +  3.402437e-59  7.781516e-56
## 223016 NC_035784.1  96023083  96023083      +  1.188683e-78  7.145950e-75
## 223140 NC_035784.1  96107107  96107107      +  1.335379e-19  9.981326e-18
## 224050 NC_035784.1  96594026  96594026      +  4.207524e-42  2.792733e-39
## 224656 NC_035785.1     22852     22852      +  2.331738e-26  3.650416e-24
## 225413 NC_035785.1   4744969   4744969      -  3.504469e-38  1.691211e-35
## 226313 NC_035785.1  12703933  12703933      -  6.137347e-31  1.510346e-28
## 228349 NC_035785.1  29830588  29830588      +  4.711217e-23  5.228255e-21
## 228532 NC_035785.1  31237990  31237990      +  6.185207e-81  4.338055e-77
## 230118 NC_035785.1  32931707  32931707      +  1.830139e-25  2.619562e-23
## 230299 NC_035785.1  33207619  33207619      -  6.147175e-22  5.976959e-20
## 231895 NC_035785.1  35764247  35764247      +  3.446737e-18  2.181771e-16
## 231961 NC_035785.1  35798192  35798192      +  1.410749e-56  2.849650e-53
## 236412 NC_035785.1  43783768  43783768      +  8.280025e-20  6.358330e-18
## 236413 NC_035785.1  43783769  43783769      -  3.161397e-50  3.736982e-47
## 236419 NC_035785.1  43840366  43840366      -  3.406505e-27  5.803689e-25
## 239594 NC_035786.1   8623470   8623470      -  4.659911e-40  2.560005e-37
## 240401 NC_035786.1  14799933  14799933      -  1.153359e-50  1.394689e-47
## 242255 NC_035786.1  33817806  33817806      +  3.839474e-34  1.250551e-31
## 242494 NC_035786.1  34083840  34083840      -  3.797446e-22  3.770706e-20
## 243041 NC_035786.1  34344322  34344322      +  1.588249e-31  4.100370e-29
## 243083 NC_035786.1  34346036  34346036      +  3.602147e-25  5.019339e-23
## 243084 NC_035786.1  34346037  34346037      -  1.606424e-67  6.500081e-64
## 243143 NC_035786.1  34361447  34361447      -  7.356602e-81  4.993184e-77
## 243256 NC_035786.1  34368875  34368875      +  1.420617e-34  4.828902e-32
## 243258 NC_035786.1  34368884  34368884      +  1.308759e-27  2.335650e-25
## 243283 NC_035786.1  34372006  34372006      -  8.252282e-65  2.800557e-61
## 244169 NC_035786.1  38651250  38651250      -  5.887889e-28  1.096013e-25
## 245336 NC_035786.1  41491818  41491818      +  3.111301e-17  1.748510e-15
## 245337 NC_035786.1  41491820  41491820      +  1.664534e-26  2.643253e-24
## 245718 NC_035786.1  42411778  42411778      -  7.667043e-23  8.272852e-21
## 245838 NC_035786.1  42447009  42447009      +  2.720933e-40  1.551506e-37
## 246107 NC_035786.1  42516043  42516043      +  7.973863e-21  6.850811e-19
## 246252 NC_035786.1  42526067  42526067      -  1.706742e-38  8.410119e-36
## 252748 NC_035786.1  57121448  57121448      -  2.192130e-25  3.108096e-23
## 253880 NC_035787.1   7167896   7167896      +  1.826038e-90  2.134515e-86
## 254551 NC_035787.1  11712232  11712232      +  2.372235e-20  1.939149e-18
## 255133 NC_035787.1  14736345  14736345      -  4.332929e-54  6.959407e-51
## 255525 NC_035787.1  18018538  18018538      -  4.723041e-46  4.089568e-43
## 255584 NC_035787.1  18058211  18058211      +  2.688025e-36  1.081418e-33
## 255991 NC_035787.1  23056764  23056764      -  5.775286e-36  2.229662e-33
## 256275 NC_035787.1  26136338  26136338      -  7.898946e-54  1.240299e-50
## 257871 NC_035787.1  33616914  33616914      +  6.070627e-21  5.297834e-19
## 259029 NC_035787.1  36375632  36375632      -  4.906782e-36  1.915446e-33
## 259341 NC_035787.1  36717473  36717473      -  5.267042e-48  5.083611e-45
## 260363 NC_035787.1  38099290  38099290      +  3.313426e-17  1.855165e-15
## 260543 NC_035787.1  40995377  40995377      +  5.281066e-21  4.647335e-19
## 260632 NC_035787.1  41013088  41013088      -  1.684350e-22  1.739816e-20
## 263079 NC_035787.1  45658937  45658937      +  7.328609e-19  5.021156e-17
## 263802 NC_035787.1  46935925  46935925      -  1.381893e-26  2.219552e-24
## 264269 NC_035787.1  47281094  47281094      -  4.120281e-28  7.820814e-26
## 264431 NC_035787.1  47493411  47493411      + 2.229543e-115 5.212371e-111
## 267367 NC_035787.1  51397493  51397493      -  1.047419e-31  2.744524e-29
## 267647 NC_035787.1  51474327  51474327      +  1.132755e-36  4.757297e-34
## 267648 NC_035787.1  51474328  51474328      -  2.279009e-63  7.051786e-60
## 267779 NC_035787.1  52112612  52112612      -  4.486074e-22  4.427323e-20
## 268601 NC_035787.1  52788270  52788270      +  6.479677e-26  9.724502e-24
## 268602 NC_035787.1  52788271  52788271      -  2.975953e-61  7.730418e-58
## 268770 NC_035787.1  52849924  52849924      +  4.828238e-67  1.881295e-63
## 269671 NC_035787.1  53342425  53342425      +  9.076980e-51  1.103970e-47
## 269776 NC_035787.1  53514334  53514334      +  2.074242e-18  1.348692e-16
## 269789 NC_035787.1  53522349  53522349      -  8.263545e-19  5.619635e-17
## 270436 NC_035787.1  55940976  55940976      +  4.853901e-17  2.670967e-15
## 270529 NC_035787.1  56242012  56242012      -  6.205249e-24  7.608585e-22
## 270649 NC_035787.1  56264109  56264109      +  2.865320e-39  1.484940e-36
## 271219 NC_035787.1  57236717  57236717      -  5.704301e-31  1.408720e-28
## 271709 NC_035787.1  59103900  59103900      -  2.822670e-49  3.109487e-46
## 271933 NC_035787.1  59437354  59437354      -  2.612318e-23  3.005206e-21
## 274244 NC_035787.1  61149803  61149803      -  1.717580e-11  4.291561e-10
## 275846 NC_035787.1  61910998  61910998      -  2.229646e-28  4.335813e-26
## 278206 NC_035787.1  70578759  70578759      +  3.571208e-44  2.732401e-41
## 278555 NC_035787.1  72586550  72586550      -  8.597641e-26  1.268591e-23
## 280015 NC_035788.1  11932781  11932781      +  1.174948e-12  3.521629e-11
## 280077 NC_035788.1  11940135  11940135      +  7.905277e-19  5.391678e-17
## 280078 NC_035788.1  11940136  11940136      -  1.862148e-59  4.305612e-56
## 280106 NC_035788.1  11942447  11942447      +  3.706436e-46  3.274053e-43
## 280520 NC_035788.1  15837301  15837301      +  6.443840e-25  8.724804e-23
## 281413 NC_035788.1  21824250  21824250      +  8.032558e-88  8.520985e-84
## 281964 NC_035788.1  35758622  35758622      -  2.724220e-29  5.772381e-27
## 282796 NC_035788.1  41246972  41246972      -  1.711138e-17  9.959525e-16
## 283584 NC_035788.1  46203998  46203998      -  6.581429e-50  7.567128e-47
## 284622 NC_035788.1  48218754  48218754      +  2.563713e-58  5.619015e-55
## 284623 NC_035788.1  48218755  48218755      -  9.462012e-20  7.205508e-18
## 284666 NC_035788.1  48219079  48219079      +  2.285793e-53  3.435349e-50
## 285305 NC_035788.1  48509356  48509356      +  7.104725e-21  6.144225e-19
## 285392 NC_035788.1  48520659  48520659      +  2.330249e-53  3.477325e-50
## 285464 NC_035788.1  48523420  48523420      +  4.808241e-56  9.197197e-53
## 285812 NC_035788.1  48573533  48573533      -  3.148784e-68  1.325058e-64
## 285827 NC_035788.1  48576355  48576355      -  2.334416e-28  4.527000e-26
## 286208 NC_035788.1  48605998  48605998      -  1.362244e-32  3.847340e-30
## 286209 NC_035788.1  48609525  48609525      -  7.069227e-19  4.848178e-17
## 286757 NC_035788.1  51732940  51732940      -  1.546409e-29  3.340622e-27
## 286928 NC_035788.1  51960234  51960234      +  3.165973e-28  6.077971e-26
## 289425 NC_035788.1  56054015  56054015      +  3.015174e-42  2.020434e-39
## 289426 NC_035788.1  56054016  56054016      -  9.376511e-49  9.671039e-46
## 289435 NC_035788.1  56054094  56054094      -  3.203337e-54  5.224863e-51
## 289436 NC_035788.1  56054103  56054103      -  2.248805e-37  9.940467e-35
## 289442 NC_035788.1  56054537  56054537      -  2.513462e-40  1.441014e-37
## 289670 NC_035788.1  56264622  56264622      +  3.212325e-29  6.732056e-27
## 289686 NC_035788.1  56266258  56266258      -  1.789173e-37  7.942111e-35
## 289688 NC_035788.1  56266322  56266322      -  4.288615e-39  2.179609e-36
## 289794 NC_035788.1  56545636  56545636      +  6.564972e-33  1.921171e-30
## 289960 NC_035788.1  56875482  56875482      -  1.729865e-26  2.734614e-24
## 291622 NC_035788.1  63489815  63489815      -  6.368421e-56  1.165188e-52
## 292344 NC_035788.1  64582354  64582354      +  4.157731e-44  3.158193e-41
## 292864 NC_035788.1  65572755  65572755      +  2.936582e-29  6.191182e-27
## 292872 NC_035788.1  65573008  65573008      -  4.304575e-38  2.039902e-35
## 293396 NC_035788.1  66163903  66163903      -  2.583239e-44  1.990966e-41
## 293564 NC_035788.1  66981277  66981277      -  3.700672e-30  8.537835e-28
## 294054 NC_035788.1  67915724  67915724      +  3.749163e-28  7.158379e-26
## 295274 NC_035788.1  70228484  70228484      +  5.504954e-25  7.540922e-23
## 295277 NC_035788.1  70228505  70228505      +  2.931793e-42  1.970838e-39
## 295295 NC_035788.1  70231743  70231743      -  9.312851e-42  6.010727e-39
## 295696 NC_035788.1  70762727  70762727      +  4.798770e-85  4.038796e-81
## 295783 NC_035788.1  70996377  70996377      -  2.784852e-38  1.353245e-35
## 296213 NC_035788.1  71239591  71239591      +  5.471647e-18  3.388104e-16
## 296242 NC_035788.1  71413851  71413851      -  2.106197e-10  4.383387e-09
## 296253 NC_035788.1  71422115  71422115      +  3.492635e-28  6.680707e-26
## 297650 NC_035788.1  75693191  75693191      -  8.561877e-29  1.730534e-26
## 297801 NC_035788.1  76059470  76059470      +  1.198637e-19  9.016900e-18
## 297802 NC_035788.1  76059473  76059473      +  1.507289e-40  8.809597e-38
## 298238 NC_035788.1  78353401  78353401      +  4.338051e-15  1.830279e-13
## 298838 NC_035788.1  80022878  80022878      -  5.513470e-48  5.297157e-45
## 298839 NC_035788.1  80022880  80022880      -  4.090328e-43  2.947388e-40
## 300204 NC_035788.1  83655136  83655136      -  4.115346e-87  3.935915e-83
## 303134 NC_035788.1 103039424 103039424      +  1.235714e-20  1.039185e-18
## 303145 NC_035788.1 103039558 103039558      -  2.161704e-22  2.202613e-20
## 304820 NC_035789.1   4864681   4864681      +  9.751803e-85  7.891755e-81
## 305346 NC_035789.1   6785228   6785228      -  2.544996e-17  1.447263e-15
## 305517 NC_035789.1   7302118   7302118      +  9.854916e-28  1.784468e-25
## 306681 NC_035789.1   9432287   9432287      +  3.866700e-53  5.689400e-50
## 306682 NC_035789.1   9432288   9432288      -  3.198947e-23  3.638290e-21
## 307034 NC_035789.1  10721394  10721394      +  1.143204e-30  2.752164e-28
## 307391 NC_035789.1  23133846  23133846      +  3.736213e-25  5.192396e-23
##        meth.diff
## 677     50.94340
## 2364   -51.04327
## 2834    53.44908
## 3329   -58.87446
## 3698    56.30202
## 3727   -57.98357
## 3739   -51.26142
## 3740   -57.90305
## 3750    50.67921
## 4576    54.72824
## 4585   -56.60468
## 7788   -50.45581
## 8149    54.89699
## 9283   -52.65900
## 10727   73.04668
## 13384  -65.30107
## 14277   50.77611
## 15236  -55.11905
## 16189   59.24065
## 16404  -53.06410
## 16504  -50.89224
## 18541  -54.50835
## 19466   52.73983
## 20393  -53.83827
## 20625   59.61388
## 20629   73.76537
## 20630   64.47744
## 22477  -52.46206
## 22482  -57.45476
## 23488   58.97228
## 23680   51.19351
## 23757   54.45935
## 23794  -54.07179
## 23935   51.84397
## 23936   50.03210
## 24023  -57.16387
## 24580   57.90551
## 26267   51.13010
## 26769   51.99773
## 26770   52.95512
## 26841   52.49685
## 30905  -57.02739
## 31771  -61.19480
## 31772  -64.28571
## 32478  -51.23117
## 34197   74.08800
## 35498   73.46519
## 35499   68.02666
## 36337   51.81395
## 36931   53.24028
## 37651   54.38837
## 39044  -52.78862
## 39153  -51.80766
## 39154  -60.95939
## 40929   51.94070
## 41205   59.78931
## 43115   52.34680
## 46173  -51.50348
## 46593  -61.68569
## 48703   56.56687
## 49787  -56.78422
## 49838   55.80670
## 49862   59.01367
## 49871   63.83230
## 50894  -50.75362
## 50940   52.58382
## 51560  -63.40251
## 52473   54.39605
## 53501   55.02359
## 54080  -52.80849
## 55540   53.86765
## 57179   50.43153
## 57545  -53.07162
## 57573   53.33333
## 58598  -61.26814
## 59827  -55.95238
## 60837  -52.19021
## 61103   53.72999
## 61104   64.08109
## 61747   53.95518
## 63331   52.80055
## 66631  -51.11329
## 68399  -50.69810
## 68646  -64.60926
## 68979   53.99211
## 68984   64.53065
## 68985   63.59188
## 70629   55.69892
## 70630   56.11490
## 70636   50.22626
## 71869  -55.72453
## 72147   56.98053
## 72149  -57.57821
## 72164  -55.53066
## 72175  -58.25464
## 72176  -59.25373
## 72184  -60.00673
## 72211  -52.86325
## 72263   52.97447
## 74940   54.35520
## 74941   56.02357
## 75217   64.41540
## 75260   51.88079
## 76886   51.51943
## 76890   69.48392
## 77258   58.72517
## 77262   54.20875
## 77438  -53.99993
## 77450   53.36485
## 77529   61.65086
## 77536   54.86797
## 79111  -54.27998
## 79276  -52.52206
## 79294  -65.61384
## 80140  -60.64998
## 80589   50.11623
## 81906  -52.23906
## 82324   51.53972
## 82326   50.32554
## 82841  -63.34688
## 84948  -59.92459
## 88238   55.59165
## 88761   51.50855
## 90375   54.50150
## 90544  -50.79017
## 91288   51.22618
## 92246   55.71336
## 94627  -54.47522
## 94628  -72.11321
## 97327   73.51043
## 97329   74.40246
## 97366  -53.42770
## 98965  -50.46313
## 99253  -52.18182
## 99880   58.00575
## 100040 -53.08333
## 100221  51.31967
## 102518 -66.12882
## 103541  52.81395
## 104280 -59.10714
## 106247 -67.66955
## 106248 -67.85236
## 108941  50.90532
## 109796  51.18566
## 110187 -50.10628
## 113079  57.07200
## 114149  52.60471
## 114150  53.74182
## 114364 -50.40440
## 121016  53.69601
## 121236  63.34808
## 121844 -52.72579
## 123743 -50.12506
## 127415 -55.00503
## 128000  50.18433
## 128301 -62.28902
## 130596 -53.89898
## 130873  51.41973
## 132517  52.27396
## 132784  50.01571
## 136680  58.23718
## 136932  58.22724
## 137735  67.57964
## 137887  51.34173
## 138382 -55.99277
## 138580  53.00408
## 138581  56.57294
## 138643  54.82143
## 138940  57.88700
## 138941  53.47388
## 138942  63.71570
## 138943  58.52923
## 139015  54.31205
## 139086 -58.16191
## 139127  65.64341
## 139136  54.49055
## 139178  56.49756
## 139695 -51.42189
## 140002 -59.11489
## 140110 -61.16667
## 140219  53.00485
## 141159 -57.39008
## 141200 -72.12389
## 142465  54.79571
## 142908 -58.01519
## 142963  55.07003
## 143044 -60.97565
## 146511  50.96154
## 146977  51.07962
## 147327 -59.95403
## 148457  52.16018
## 148458  54.58333
## 148988  53.53083
## 150110  57.12876
## 150654  55.03071
## 150655  57.44298
## 151588 -57.77001
## 156696 -50.11687
## 156816  59.53624
## 156882 -65.24510
## 157293  57.13468
## 157505 -56.65267
## 158415  56.34738
## 158681 -62.49035
## 158710  51.74208
## 159095 -63.00665
## 159325 -59.92498
## 159355 -60.62009
## 159439 -60.03490
## 159485 -57.16685
## 159695 -54.94580
## 159959 -57.80114
## 160330  56.17387
## 161194 -64.35295
## 162080  53.40161
## 162626 -50.65524
## 164573 -56.68699
## 166794  55.94747
## 168963  57.35119
## 170678 -58.13427
## 172233  53.37813
## 172428  59.78534
## 173841 -55.53708
## 174140 -52.19282
## 174141 -59.73063
## 176356  62.07729
## 178861  51.88324
## 179311 -61.47751
## 182037  55.94429
## 183909 -50.37594
## 186158  52.28198
## 187151  64.14072
## 187153  54.28599
## 187245 -52.38961
## 187246 -52.80148
## 187266 -75.65022
## 187267 -68.59023
## 189739  50.68619
## 190488  50.56497
## 191247 -51.76288
## 191514  60.63987
## 192152 -51.73233
## 192153 -51.52164
## 193010 -58.81369
## 193012 -51.17107
## 193890  59.81555
## 194523  57.35516
## 194525  51.08881
## 194734 -55.89721
## 195142 -51.41949
## 195180 -51.45025
## 195917 -50.27778
## 196178  61.70722
## 196229  67.86164
## 196810  60.32476
## 196811  63.04585
## 197684 -51.55383
## 198015 -64.92072
## 198053  53.39217
## 198542  56.37678
## 198670  52.98686
## 200203  52.30589
## 206634 -57.16717
## 206694  56.34287
## 206695  69.20753
## 207194 -59.67169
## 210454  55.34894
## 212585 -57.63158
## 212590 -50.85063
## 212722  50.21400
## 213122  55.94705
## 213126 -55.31673
## 213127 -53.54567
## 213328 -50.54348
## 214512 -51.20690
## 215424 -51.52653
## 215966  50.05769
## 215973 -53.73411
## 218093 -61.34221
## 218313  51.49551
## 218712 -64.13814
## 219310 -52.67291
## 219311 -54.81687
## 219617 -65.16353
## 219795 -74.76383
## 219796 -59.77553
## 220702 -50.00878
## 222930  54.76629
## 223008 -56.62279
## 223016  60.73899
## 223140  51.38274
## 224050 -63.63636
## 224656 -51.10902
## 225413  63.56600
## 226313  60.07357
## 228349  53.88140
## 228532  55.32544
## 230118 -59.63069
## 230299  59.87403
## 231895  52.15686
## 231961 -54.58120
## 236412  52.17918
## 236413  57.15486
## 236419  50.20635
## 239594 -60.78519
## 240401 -61.36364
## 242255  55.10723
## 242494 -59.20379
## 243041 -50.34792
## 243083  55.94937
## 243084  58.80736
## 243143  71.45428
## 243256 -58.04344
## 243258 -52.05639
## 243283  50.70286
## 244169 -51.36836
## 245336 -56.40271
## 245337  63.66714
## 245718 -50.67791
## 245838 -59.91674
## 246107  53.03618
## 246252  51.44439
## 252748  59.01624
## 253880  55.82944
## 254551 -51.94497
## 255133  54.69086
## 255525  53.21802
## 255584 -51.65707
## 255991 -55.16576
## 256275 -71.37716
## 257871  52.38176
## 259029  54.29802
## 259341 -51.55593
## 260363 -51.20453
## 260543  60.84991
## 260632 -51.91276
## 263079 -51.84443
## 263802 -50.91188
## 264269  55.19980
## 264431 -51.44680
## 267367 -55.79187
## 267647 -56.39185
## 267648 -60.52849
## 267779 -51.65450
## 268601 -54.94582
## 268602 -51.60033
## 268770 -56.49066
## 269671 -52.30656
## 269776  58.14296
## 269789 -50.17784
## 270436  50.29045
## 270529 -55.62016
## 270649 -51.71702
## 271219 -56.53678
## 271709 -62.45818
## 271933 -57.97462
## 274244 -50.75066
## 275846 -61.22449
## 278206 -64.27277
## 278555  50.22791
## 280015 -50.78491
## 280077  53.76448
## 280078  53.14266
## 280106 -63.33333
## 280520 -51.25247
## 281413 -53.39553
## 281964  56.03104
## 282796  50.46366
## 283584 -56.74397
## 284622  63.79478
## 284623  52.00219
## 284666  56.50932
## 285305 -54.51744
## 285392  53.57011
## 285464  66.37443
## 285812  55.14231
## 285827  54.06351
## 286208 -53.25819
## 286209  51.24229
## 286757  57.96778
## 286928 -50.83367
## 289425  54.97454
## 289426  52.68717
## 289435 -63.27756
## 289436 -57.95124
## 289442 -50.95332
## 289670  52.05773
## 289686  52.65568
## 289688  52.07270
## 289794  50.82633
## 289960 -50.63495
## 291622  61.28207
## 292344 -68.16093
## 292864  52.24431
## 292872  52.74704
## 293396  59.95917
## 293564  55.66343
## 294054 -51.66667
## 295274 -50.99469
## 295277  63.55876
## 295295  54.88445
## 295696  50.21260
## 295783  67.52190
## 296213  54.01989
## 296242 -50.22260
## 296253 -64.40139
## 297650  51.34788
## 297801 -50.97781
## 297802 -69.32515
## 298238 -52.51647
## 298838  56.15201
## 298839  54.99525
## 300204  60.75166
## 303134 -52.40113
## 303145  53.88199
## 304820  66.54924
## 305346  52.17822
## 305517 -54.94260
## 306681 -56.70921
## 306682 -53.53965
## 307034  56.24641
## 307391 -52.61376
write.table(myDiff50p, file = "../analyses/myDiff50p.tab", sep = "\t")

Taking the DMLs to a bed

library(readr)
myDiff50p <- read_csv("../analyses/myDiff50p.csv")
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
##   X1 = col_integer(),
##   chr = col_character(),
##   start = col_integer(),
##   end = col_integer(),
##   strand = col_character(),
##   pvalue = col_double(),
##   qvalue = col_double(),
##   meth.diff = col_double()
## )
head(myDiff50p)
## # A tibble: 6 x 8
##      X1 chr           start     end strand   pvalue   qvalue meth.diff
##   <int> <chr>         <int>   <int> <chr>     <dbl>    <dbl>     <dbl>
## 1   677 NC_035780.1  346073  346073 -      2.66e-24 3.40e-22      50.9
## 2  2364 NC_035780.1  990997  990997 -      2.73e-29 5.78e-27     -51.0
## 3  2834 NC_035780.1 1959000 1959000 -      3.96e-85 3.47e-81      53.4
## 4  3329 NC_035780.1 2541728 2541728 -      1.18e-26 1.91e-24     -58.9
## 5  3698 NC_035780.1 2584493 2584493 +      6.35e-56 1.17e-52      56.3
## 6  3727 NC_035780.1 2586510 2586510 -      1.06e-35 3.98e-33     -58.0
library(tidyverse)
## ── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
## ✔ ggplot2 2.2.1     ✔ purrr   0.2.4
## ✔ tibble  1.4.2     ✔ dplyr   0.7.4
## ✔ tidyr   0.8.0     ✔ stringr 1.3.1
## ✔ ggplot2 2.2.1     ✔ forcats 0.3.0
## ── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::collapse()   masks IRanges::collapse()
## ✖ dplyr::combine()    masks BiocGenerics::combine()
## ✖ dplyr::desc()       masks IRanges::desc()
## ✖ tidyr::expand()     masks S4Vectors::expand()
## ✖ dplyr::filter()     masks stats::filter()
## ✖ dplyr::first()      masks S4Vectors::first()
## ✖ dplyr::lag()        masks stats::lag()
## ✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position()
## ✖ purrr::reduce()     masks GenomicRanges::reduce(), IRanges::reduce()
## ✖ dplyr::rename()     masks S4Vectors::rename()
## ✖ dplyr::select()     masks methylKit::select()
## ✖ dplyr::slice()      masks IRanges::slice()
## ✖ tidyr::unite()      masks methylKit::unite()
dml05251200plus <- filter(myDiff50p, strand == "+") %>% mutate(start = start -1, end = end + 1) %>% select(chr, start, end, strand, meth.diff)
## Warning: package 'bindrcpp' was built under R version 3.4.4
dml05251200minus <- filter(myDiff50p, strand == "-") %>% mutate(start = start -2) %>% select(chr, start, end, strand, meth.diff)

dml05251200.bed <- bind_rows(dml05251200plus, dml05251200minus) %>% arrange(chr, start) %>%
  mutate_if(is.numeric, as.integer)
#latter was done to refrain from writing as scientific notation


dml05251200.bed
## # A tibble: 422 x 5
##    chr           start     end strand meth.diff
##    <chr>         <int>   <int> <chr>      <int>
##  1 NC_035780.1  346071  346073 -             50
##  2 NC_035780.1  990995  990997 -            -51
##  3 NC_035780.1 1958998 1959000 -             53
##  4 NC_035780.1 2541726 2541728 -            -58
##  5 NC_035780.1 2584492 2584494 +             56
##  6 NC_035780.1 2586508 2586510 -            -57
##  7 NC_035780.1 2588794 2588796 +            -51
##  8 NC_035780.1 2588794 2588796 -            -57
##  9 NC_035780.1 2589720 2589722 -             50
## 10 NC_035780.1 4286286 4286288 +             54
## # ... with 412 more rows
write_delim(dml05251200.bed, "../analyses/dml05251200.bed",  delim = '\t', col_names = FALSE)
Written on May 25, 2018