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CpG interval report generated on 20/05/20 with pycoMeth 0.4.6
Interval details
| pvalue rank | chromosome | start | end | length | number of samples | number of CpGs | pvalue | adjusted pvalue |
|---|---|---|---|---|---|---|---|---|
| #167 | 10 | 101778627 | 101780425 | 1798 | 3 | 56 | 7.31885e-15 | 4.35844e-13 |
Methylation log-likelihood ratio by CpG position
Distribution of CpG methylation log-likelihood ratio by sample
Closest transcripts TSS
| distance to tss | transcript id | gene id | transcript name | chromosome | start | end | strand | feature type | transcript biotype |
|---|---|---|---|---|---|---|---|---|---|
| 0 | enst00000618991 | sg00000107831 | fgf8-207 | 10 | 101770130 | 101780369 | - | mRNA | protein_coding |
| 2223 | enst00000468544 | sg00000107833 | npm3-203 | 10 | 101781727 | 101782648 | - | lnc_RNA | processed_transcript |
| -2513 | enst00000344255 | sg00000107831 | fgf8-202 | 10 | 101770131 | 101776114 | - | mRNA | protein_coding |
| -2530 | enst00000469792 | sg00000107831 | fgf8-205 | 10 | 101770142 | 101776097 | - | mRNA | nonsense_mediated_decay |
| -2557 | enst00000347978 | sg00000107831 | fgf8-204 | 10 | 101770324 | 101776070 | - | mRNA | protein_coding |
| -2653 | enst00000346714 | sg00000107831 | fgf8-203 | 10 | 101770324 | 101775974 | - | mRNA | protein_coding |
| -2668 | enst00000320185 | sg00000107831 | fgf8-201 | 10 | 101770324 | 101775959 | - | mRNA | protein_coding |
| -2727 | enst00000485728 | sg00000107831 | fgf8-206 | 10 | 101770324 | 101775900 | - | lnc_RNA | processed_transcript |
| 2950 | enst00000462391 | sg00000107833 | npm3-202 | 10 | 101781589 | 101783375 | - | lnc_RNA | processed_transcript |
| 2959 | enst00000474993 | sg00000107833 | npm3-204 | 10 | 101781332 | 101783384 | - | lnc_RNA | processed_transcript |
| 2988 | enst00000370110 | sg00000107833 | npm3-201 | 10 | 101781325 | 101783413 | - | mRNA | protein_coding |
| 7540 | enst00000462994 | sg00000198408 | oga-207 | 10 | 101786102 | 101787965 | - | lnc_RNA | processed_transcript |
| 11028 | enst00000461645 | sg00000198408 | oga-206 | 10 | 101786563 | 101791453 | - | lnc_RNA | processed_transcript |
| 12521 | enst00000494347 | sg00000198408 | oga-211 | 10 | 101786144 | 101792946 | - | lnc_RNA | processed_transcript |
| 13670 | enst00000492204 | sg00000198408 | oga-210 | 10 | 101792608 | 101794095 | - | lnc_RNA | processed_transcript |
| 17592 | enst00000479811 | sg00000198408 | oga-208 | 10 | 101786534 | 101798017 | - | lnc_RNA | processed_transcript |
| 18907 | enst00000482611 | sg00000198408 | oga-209 | 10 | 101786134 | 101799332 | - | lnc_RNA | processed_transcript |
| 37441 | enst00000429860 | sg00000198408 | oga-204 | 10 | 101803747 | 101817866 | - | mRNA | protein_coding |
| 37993 | enst00000357797 | sg00000198408 | oga-201 | 10 | 101786134 | 101818418 | - | mRNA | protein_coding |
| 37993 | enst00000370094 | sg00000198408 | oga-203 | 10 | 101797046 | 101818418 | - | mRNA | protein_coding |
| 38019 | enst00000361464 | sg00000198408 | oga-202 | 10 | 101784450 | 101818444 | - | mRNA | protein_coding |
| 38040 | enst00000439817 | sg00000198408 | oga-205 | 10 | 101784443 | 101818465 | - | mRNA | protein_coding |
| 38375 | enst00000412353 | sg00000226009 | kcnip2-as1-201 | 10 | 101818800 | 101828885 | + | lnc_RNA | lncrna |
| 47530 | enst00000460388 | sg00000120049 | kcnip2-210 | 10 | 101826973 | 101827955 | - | lnc_RNA | processed_transcript |
| -48590 | enst00000664847 | sg00000224817 | ac010789.1-202 | 10 | 101701998 | 101730037 | - | lnc_RNA | lncrna |
| -48590 | enst00000670664 | sg00000224817 | ac010789.1-203 | 10 | 101701994 | 101730037 | - | lnc_RNA | lncrna |
| 49122 | enst00000483385 | sg00000120049 | kcnip2-213 | 10 | 101828267 | 101829547 | - | lnc_RNA | processed_transcript |
| 50013 | enst00000434163 | sg00000120049 | kcnip2-209 | 10 | 101827353 | 101830438 | - | mRNA | protein_coding |
| 53944 | enst00000642874 | sg00000120049 | kcnip2-214 | 10 | 101827353 | 101834369 | - | mRNA | protein_coding |
| 59447 | enst00000348850 | sg00000120049 | kcnip2-203 | 10 | 101825974 | 101839872 | - | mRNA | protein_coding |
| 63143 | enst00000472764 | sg00000120049 | kcnip2-212 | 10 | 101827296 | 101843568 | - | lnc_RNA | processed_transcript |
| 63143 | enst00000239117 | sg00000120049 | kcnip2-201 | 10 | 101827641 | 101843568 | - | mRNA | protein_coding |
| 63143 | enst00000461105 | sg00000120049 | kcnip2-211 | 10 | 101827353 | 101843568 | - | mRNA | protein_coding |
| 63143 | enst00000353068 | sg00000120049 | kcnip2-204 | 10 | 101827353 | 101843568 | - | mRNA | protein_coding |
| 63143 | enst00000343195 | sg00000120049 | kcnip2-202 | 10 | 101827353 | 101843568 | - | mRNA | protein_coding |
| 63344 | enst00000370046 | sg00000120049 | kcnip2-208 | 10 | 101827186 | 101843769 | - | mRNA | protein_coding |
| 63419 | enst00000356640 | sg00000120049 | kcnip2-206 | 10 | 101826453 | 101843844 | - | mRNA | protein_coding |
| 63495 | enst00000358038 | sg00000120049 | kcnip2-207 | 10 | 101825975 | 101843920 | - | mRNA | protein_coding |
| 63495 | enst00000355657 | sg00000120049 | kcnip2-205 | 10 | 101825974 | 101843920 | - | lnc_RNA | processed_transcript |
| -70226 | enst00000458489 | sg00000224817 | ac010789.1-201 | 10 | 101704652 | 101708401 | - | lnc_RNA | lncrna |
| -83332 | enst00000457105 | sg00000107829 | fbxw4-202 | 10 | 101624747 | 101695295 | - | lnc_RNA | processed_transcript |
| -83368 | enst00000664783 | sg00000107829 | fbxw4-206 | 10 | 101610667 | 101695259 | - | mRNA | protein_coding |
| -83457 | enst00000331272 | sg00000107829 | fbxw4-201 | 10 | 101610666 | 101695170 | - | mRNA | protein_coding |
| -84226 | enst00000663752 | sg00000286489 | ac010789.2-201 | 10 | 101694401 | 101705119 | + | lnc_RNA | lncrna |
| -101913 | enst00000489578 | sg00000107829 | fbxw4-205 | 10 | 101673565 | 101676714 | - | lnc_RNA | retained_intron |
| 109311 | enst00000495001 | sg00000120029 | armh3-205 | 10 | 101845599 | 101889736 | - | lnc_RNA | processed_transcript |
| 132854 | enst00000615609 | sg00000274742 | al391827.2-201 | 10 | 101912998 | 101913279 | - | ncRNA | misc_rna |
| -151728 | enst00000470093 | sg00000107829 | fbxw4-203 | 10 | 101610664 | 101626899 | - | lnc_RNA | processed_transcript |
| -155768 | enst00000410119 | sg00000222051 | rnu6-1165p-201 | 10 | 101622859 | 101622965 | + | snRNA | snrna |
| -165474 | enst00000482428 | sg00000107829 | fbxw4-204 | 10 | 101611657 | 101613153 | - | lnc_RNA | processed_transcript |
| 172279 | enst00000410498 | sg00000222430 | al391827.1-201 | 10 | 101952605 | 101952704 | - | ncRNA | misc_rna |
| -177130 | enst00000637571 | sg00000283558 | mir3158-2-201 | 10 | 101601417 | 101601497 | - | miRNA | mirna |
| -177210 | enst00000583596 | sg00000263436 | mir3158-1-201 | 10 | 101601417 | 101601497 | + | miRNA | mirna |
| -177888 | enst00000475443 | sg00000166171 | dpcd-205 | 10 | 101600739 | 101609661 | + | lnc_RNA | processed_transcript |
| -183925 | enst00000434727 | sg00000166171 | dpcd-203 | 10 | 101594702 | 101609439 | + | mRNA | protein_coding |
| -190302 | enst00000370147 | sg00000166171 | dpcd-201 | 10 | 101588325 | 101609447 | + | mRNA | protein_coding |
| -190306 | enst00000370151 | sg00000166171 | dpcd-202 | 10 | 101588321 | 101609662 | + | mRNA | protein_coding |
| -190318 | enst00000626968 | sg00000166171 | dpcd-206 | 10 | 101588309 | 101608902 | + | mRNA | protein_coding |
| -190357 | enst00000628479 | sg00000166169 | poll-217 | 10 | 101578884 | 101588270 | - | mRNA | protein_coding |
| -190370 | enst00000370162 | sg00000166169 | poll-203 | 10 | 101578882 | 101588257 | - | mRNA | protein_coding |
| -190379 | enst00000370172 | sg00000166169 | poll-206 | 10 | 101578882 | 101588248 | - | mRNA | protein_coding |
| -190385 | enst00000461587 | sg00000166169 | poll-213 | 10 | 101584794 | 101588242 | - | lnc_RNA | processed_transcript |
| -190395 | enst00000430045 | sg00000166169 | poll-211 | 10 | 101585324 | 101588232 | - | mRNA | protein_coding |
| -190395 | enst00000429502 | sg00000166169 | poll-210 | 10 | 101579696 | 101588232 | - | mRNA | protein_coding |
| -190397 | enst00000413344 | sg00000166169 | poll-207 | 10 | 101584687 | 101588230 | - | mRNA | protein_coding |
| -190399 | enst00000470140 | sg00000166169 | poll-215 | 10 | 101580252 | 101588228 | - | lnc_RNA | processed_transcript |
| -190418 | enst00000299206 | sg00000166169 | poll-201 | 10 | 101578882 | 101588209 | - | mRNA | protein_coding |
| -190501 | enst00000339310 | sg00000166169 | poll-202 | 10 | 101578882 | 101588126 | - | mRNA | protein_coding |
| -191206 | enst00000370169 | sg00000166169 | poll-205 | 10 | 101578882 | 101587421 | - | mRNA | protein_coding |
| -191221 | enst00000415897 | sg00000166169 | poll-208 | 10 | 101579515 | 101587406 | - | mRNA | protein_coding |
| -191222 | enst00000426919 | sg00000166169 | poll-209 | 10 | 101583602 | 101587405 | - | mRNA | protein_coding |
| -191427 | enst00000454524 | sg00000166169 | poll-212 | 10 | 101584611 | 101587200 | - | mRNA | protein_coding |
| -193708 | enst00000485369 | sg00000166169 | poll-216 | 10 | 101579675 | 101584919 | - | lnc_RNA | processed_transcript |
| -195434 | enst00000370168 | sg00000166169 | poll-204 | 10 | 101578882 | 101583193 | - | mRNA | protein_coding |
| -196402 | enst00000463515 | sg00000166169 | poll-214 | 10 | 101578882 | 101582225 | - | lnc_RNA | processed_transcript |
| -208067 | enst00000470165 | sg00000166171 | dpcd-204 | 10 | 101570560 | 101596651 | + | lnc_RNA | processed_transcript |
| 221639 | enst00000456149 | sg00000120029 | armh3-203 | 10 | 101990551 | 102002064 | - | mRNA | protein_coding |
| -243243 | enst00000493877 | sg00000166167 | btrc-207 | 10 | 101535384 | 101551191 | + | lnc_RNA | processed_transcript |
| 253013 | enst00000470043 | sg00000120029 | armh3-204 | 10 | 102029448 | 102033438 | - | lnc_RNA | processed_transcript |
| 275748 | enst00000370033 | sg00000120029 | armh3-202 | 10 | 101845599 | 102056173 | - | mRNA | protein_coding |
| 275768 | enst00000311122 | sg00000120029 | armh3-201 | 10 | 102029448 | 102056193 | - | mRNA | protein_coding |
| 284924 | enst00000299238 | sg00000166189 | hps6-201 | 10 | 102065349 | 102068036 | + | mRNA | protein_coding |
| 305305 | enst00000448532 | sg00000224302 | al500527.1-201 | 10 | 102085476 | 102085730 | - | pseudogenic_transcript | processed_pseudogene |
| 309543 | enst00000454105 | sg00000229629 | al500527.2-201 | 10 | 102089968 | 102090062 | + | pseudogenic_transcript | processed_pseudogene |
| 330708 | enst00000461873 | sg00000198728 | ldb1-203 | 10 | 102110392 | 102111133 | - | lnc_RNA | processed_transcript |
| 334521 | enst00000361198 | sg00000198728 | ldb1-201 | 10 | 102107560 | 102114946 | - | mRNA | protein_coding |
| 339860 | enst00000425280 | sg00000198728 | ldb1-202 | 10 | 102107560 | 102120285 | - | mRNA | protein_coding |
| 339943 | enst00000673968 | sg00000198728 | ldb1-204 | 10 | 102106489 | 102120368 | - | mRNA | protein_coding |
| 352569 | enst00000413464 | sg00000148840 | pprc1-203 | 10 | 102132994 | 102150331 | + | mRNA | protein_coding |
| 352615 | enst00000278070 | sg00000148840 | pprc1-201 | 10 | 102133040 | 102150333 | + | mRNA | protein_coding |
| 361067 | enst00000370012 | sg00000148840 | pprc1-202 | 10 | 102141492 | 102150180 | + | mRNA | protein_coding |
| 361330 | enst00000489648 | sg00000148840 | pprc1-205 | 10 | 102141755 | 102149220 | + | lnc_RNA | processed_transcript |
| 362530 | enst00000462933 | sg00000148840 | pprc1-204 | 10 | 102142955 | 102144834 | + | lnc_RNA | processed_transcript |
| 367968 | enst00000495914 | sg00000148840 | pprc1-206 | 10 | 102148393 | 102149317 | + | lnc_RNA | processed_transcript |
| 371751 | enst00000605788 | sg00000166197 | nolc1-209 | 10 | 102152176 | 102163866 | + | mRNA | protein_coding |
| 371751 | enst00000405356 | sg00000166197 | nolc1-202 | 10 | 102152176 | 102163871 | + | mRNA | protein_coding |
| 371970 | enst00000464969 | sg00000166197 | nolc1-204 | 10 | 102152395 | 102162599 | + | mRNA | nonsense_mediated_decay |
| 371979 | enst00000488254 | sg00000166197 | nolc1-207 | 10 | 102152404 | 102162600 | + | mRNA | protein_coding |
| 371979 | enst00000603946 | sg00000166197 | nolc1-208 | 10 | 102152404 | 102163866 | + | mRNA | nonsense_mediated_decay |
| 371984 | enst00000461421 | sg00000166197 | nolc1-203 | 10 | 102152409 | 102160559 | + | mRNA | protein_coding |
| 371988 | enst00000476468 | sg00000166197 | nolc1-205 | 10 | 102152413 | 102159938 | + | mRNA | protein_coding |
| 371990 | enst00000370007 | sg00000166197 | nolc1-201 | 10 | 102152415 | 102163870 | + | mRNA | protein_coding |
| 380305 | enst00000477977 | sg00000166197 | nolc1-206 | 10 | 102160730 | 102163866 | + | lnc_RNA | processed_transcript |
| -413592 | enst00000410482 | sg00000222414 | rnu2-59p-201 | 10 | 101364845 | 101365035 | - | snRNA | snrna |
| -424093 | enst00000370183 | sg00000166167 | btrc-201 | 10 | 101354534 | 101526083 | + | mRNA | protein_coding |
| -424445 | enst00000465182 | sg00000166167 | btrc-205 | 10 | 101354182 | 101526194 | + | lnc_RNA | processed_transcript |
| -424462 | enst00000370187 | sg00000166167 | btrc-202 | 10 | 101354165 | 101557313 | + | mRNA | protein_coding |
| -424520 | enst00000408038 | sg00000166167 | btrc-204 | 10 | 101354107 | 101557321 | + | mRNA | protein_coding |
| -424558 | enst00000475200 | sg00000166167 | btrc-206 | 10 | 101354069 | 101521712 | + | lnc_RNA | processed_transcript |
| -424594 | enst00000393441 | sg00000166167 | btrc-203 | 10 | 101354033 | 101557319 | + | mRNA | protein_coding |
| 445874 | enst00000370005 | sg00000119915 | elovl3-201 | 10 | 102226299 | 102229589 | + | mRNA | protein_coding |
| 451658 | enst00000539804 | sg00000107859 | pitx3-202 | 10 | 102230186 | 102232083 | - | mRNA | protein_coding |
| -455233 | enst00000450669 | sg00000230967 | al133387.2-201 | 10 | 101322485 | 101323394 | - | lnc_RNA | lncrna |
| 461087 | enst00000370002 | sg00000107859 | pitx3-201 | 10 | 102230189 | 102241512 | - | mRNA | protein_coding |
| 465107 | enst00000369983 | sg00000107862 | gbf1-201 | 10 | 102245532 | 102382899 | + | mRNA | protein_coding |
| 465107 | enst00000674034 | sg00000107862 | gbf1-204 | 10 | 102245532 | 102382899 | + | mRNA | protein_coding |
| 465107 | enst00000673650 | sg00000107862 | gbf1-203 | 10 | 102245532 | 102382899 | + | mRNA | protein_coding |
| -467609 | enst00000442188 | sg00000225208 | al133387.1-201 | 10 | 101311018 | 101311505 | + | lnc_RNA | lncrna |
| -471098 | enst00000410306 | sg00000222238 | rnu2-43p-201 | 10 | 101307529 | 101307718 | + | snRNA | snrna |
Source file: /hps/research1/birney/users/adrien/analyses/cancer_DNA_promethion/run_1_2_3_4/DNA_pipeline_2/results/methylation/pycometh_meth_comp_CGI_3/out.tsv.gz
MD5 hash: 9aa0e3f69cb4e12345c3758eb68a5efc