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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 |
|---|---|---|---|---|---|---|---|---|
| #172 | 15 | 93065800 | 93066857 | 1057 | 3 | 33 | 1.08935e-14 | 6.29862e-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 | enst00000557561 | sg00000258611 | ac087641.1-201 | 15 | 93065586 | 93066606 | - | pseudogenic_transcript | transcribed_processed_pseudogene |
| -2731 | enst00000555584 | sg00000182175 | rgma-206 | 15 | 93052272 | 93063069 | - | lnc_RNA | processed_transcript |
| 6277 | enst00000557608 | sg00000182175 | rgma-212 | 15 | 93066006 | 93073134 | - | lnc_RNA | retained_intron |
| 6288 | enst00000557420 | sg00000182175 | rgma-211 | 15 | 93044947 | 93073145 | - | mRNA | protein_coding |
| 6291 | enst00000542321 | sg00000182175 | rgma-203 | 15 | 93043416 | 93073148 | - | mRNA | protein_coding |
| 6806 | enst00000556658 | sg00000182175 | rgma-208 | 15 | 93044956 | 93073663 | - | mRNA | protein_coding |
| 6823 | enst00000554387 | sg00000182175 | rgma-205 | 15 | 93043417 | 93073680 | - | mRNA | nonsense_mediated_decay |
| 6853 | enst00000425933 | sg00000182175 | rgma-202 | 15 | 93043406 | 93073710 | - | mRNA | protein_coding |
| -6959 | enst00000650169 | sg00000182175 | rgma-213 | 15 | 93044749 | 93058841 | - | lnc_RNA | processed_transcript |
| 7271 | enst00000557301 | sg00000182175 | rgma-210 | 15 | 93044818 | 93074128 | - | mRNA | protein_coding |
| 21666 | enst00000555598 | sg00000182175 | rgma-207 | 15 | 93052320 | 93088523 | - | mRNA | protein_coding |
| 21666 | enst00000543599 | sg00000182175 | rgma-204 | 15 | 93043406 | 93088523 | - | mRNA | protein_coding |
| 21796 | enst00000556950 | sg00000182175 | rgma-209 | 15 | 93072967 | 93088653 | - | mRNA | protein_coding |
| 22347 | enst00000329082 | sg00000182175 | rgma-201 | 15 | 93035273 | 93089204 | - | mRNA | protein_coding |
| -53372 | enst00000627460 | sg00000173575 | chd2-211 | 15 | 93012428 | 93024742 | + | mRNA | nonsense_mediated_decay |
| -61287 | enst00000630813 | sg00000173575 | chd2-220 | 15 | 93004513 | 93009357 | + | lnc_RNA | retained_intron |
| -68484 | enst00000635922 | sg00000173575 | chd2-222 | 15 | 92997316 | 92998002 | + | lnc_RNA | processed_transcript |
| -68498 | enst00000629104 | sg00000173575 | chd2-216 | 15 | 92997302 | 93004646 | + | mRNA | nonsense_mediated_decay |
| -68728 | enst00000625662 | sg00000173575 | chd2-205 | 15 | 92997072 | 93027942 | + | mRNA | nonsense_mediated_decay |
| -68846 | enst00000627185 | sg00000173575 | chd2-209 | 15 | 92996954 | 92997643 | + | lnc_RNA | retained_intron |
| -81341 | enst00000637789 | sg00000173575 | chd2-229 | 15 | 92984459 | 93000535 | + | mRNA | nonsense_mediated_decay |
| -91071 | enst00000636306 | sg00000173575 | chd2-223 | 15 | 92974729 | 93002234 | + | lnc_RNA | processed_transcript |
| -91811 | enst00000636410 | sg00000173575 | chd2-224 | 15 | 92973989 | 92974925 | + | lnc_RNA | processed_transcript |
| -93917 | enst00000625463 | sg00000173575 | chd2-204 | 15 | 92971883 | 92979207 | + | mRNA | protein_coding |
| -93917 | enst00000628118 | sg00000173575 | chd2-213 | 15 | 92971883 | 92979213 | + | lnc_RNA | processed_transcript |
| -109248 | enst00000627200 | sg00000173575 | chd2-210 | 15 | 92956552 | 92965373 | + | lnc_RNA | processed_transcript |
| 113142 | enst00000647994 | sg00000285663 | ac108457.1-201 | 15 | 93177269 | 93179999 | - | lnc_RNA | lncrna |
| -115398 | enst00000628181 | sg00000173575 | chd2-214 | 15 | 92950402 | 92967341 | + | lnc_RNA | processed_transcript |
| -119960 | enst00000630016 | sg00000173575 | chd2-219 | 15 | 92945840 | 92949229 | + | mRNA | nonsense_mediated_decay |
| -122860 | enst00000625243 | sg00000173575 | chd2-203 | 15 | 92942940 | 92946168 | + | mRNA | protein_coding |
| -126144 | enst00000636881 | sg00000173575 | chd2-226 | 15 | 92939656 | 93000635 | + | mRNA | nonsense_mediated_decay |
| -126146 | enst00000637613 | sg00000173575 | chd2-228 | 15 | 92939654 | 92949228 | + | mRNA | protein_coding |
| -141522 | enst00000637572 | sg00000173575 | chd2-227 | 15 | 92924278 | 92997069 | + | lnc_RNA | retained_intron |
| -144423 | enst00000636861 | sg00000173575 | chd2-225 | 15 | 92921377 | 92924385 | + | lnc_RNA | processed_transcript |
| -150826 | enst00000629136 | sg00000173575 | chd2-217 | 15 | 92914974 | 92937588 | + | lnc_RNA | processed_transcript |
| -161327 | enst00000626782 | sg00000173575 | chd2-207 | 15 | 92904473 | 92949231 | + | mRNA | protein_coding |
| -161401 | enst00000577670 | sg00000284324 | mir3175-201 | 15 | 92904399 | 92904475 | + | miRNA | mirna |
| 163177 | enst00000670300 | sg00000257060 | ac091078.1-214 | 15 | 93230034 | 93251480 | + | lnc_RNA | lncrna |
| 164825 | enst00000667030 | sg00000257060 | ac091078.1-211 | 15 | 93231682 | 93541205 | + | lnc_RNA | lncrna |
| -165458 | enst00000625990 | sg00000173575 | chd2-206 | 15 | 92900342 | 92972318 | + | mRNA | protein_coding |
| -165476 | enst00000394196 | sg00000173575 | chd2-201 | 15 | 92900324 | 93027996 | + | mRNA | protein_coding |
| -165476 | enst00000635856 | sg00000173575 | chd2-221 | 15 | 92900324 | 92993235 | + | lnc_RNA | processed_transcript |
| -165476 | enst00000628375 | sg00000173575 | chd2-215 | 15 | 92900324 | 92947577 | + | mRNA | protein_coding |
| -165476 | enst00000629346 | sg00000173575 | chd2-218 | 15 | 92900324 | 92902788 | + | mRNA | protein_coding |
| -165476 | enst00000420239 | sg00000173575 | chd2-202 | 15 | 92900324 | 92949234 | + | mRNA | protein_coding |
| -165479 | enst00000627622 | sg00000173575 | chd2-212 | 15 | 92900321 | 92902402 | + | mRNA | protein_coding |
| -165611 | enst00000626874 | sg00000173575 | chd2-208 | 15 | 92900189 | 93022162 | + | mRNA | protein_coding |
| -178044 | enst00000555520 | sg00000272888 | linc01578-206 | 15 | 92887756 | 92898072 | + | lnc_RNA | lncrna |
| -179597 | enst00000630790 | sg00000279765 | ac013394.1-202 | 15 | 92886203 | 92949230 | + | lnc_RNA | retained_intron |
| -180476 | enst00000555227 | sg00000272888 | linc01578-205 | 15 | 92885324 | 92886985 | + | lnc_RNA | retained_intron |
| -181429 | enst00000554133 | sg00000272888 | linc01578-202 | 15 | 92884371 | 92898130 | + | lnc_RNA | retained_intron |
| -182387 | enst00000629685 | sg00000279765 | ac013394.1-201 | 15 | 92883413 | 92927330 | + | mRNA | protein_coding |
| -182785 | enst00000557147 | sg00000272888 | linc01578-208 | 15 | 92883015 | 92886222 | + | lnc_RNA | lncrna |
| -182912 | enst00000554894 | sg00000272888 | linc01578-204 | 15 | 92882888 | 92892034 | + | lnc_RNA | lncrna |
| -182926 | enst00000554669 | sg00000272888 | linc01578-203 | 15 | 92882874 | 92885584 | + | lnc_RNA | lncrna |
| -182938 | enst00000556895 | sg00000272888 | linc01578-207 | 15 | 92882862 | 92897975 | + | lnc_RNA | lncrna |
| -183068 | enst00000553829 | sg00000272888 | linc01578-201 | 15 | 92882732 | 92883861 | + | lnc_RNA | lncrna |
| -183093 | enst00000557682 | sg00000272888 | linc01578-209 | 15 | 92882707 | 92899701 | + | lnc_RNA | lncrna |
| 190341 | enst00000555297 | sg00000258888 | ac112693.1-201 | 15 | 93257198 | 93260475 | + | lnc_RNA | lncrna |
| 234790 | enst00000556538 | sg00000258971 | ac112693.2-201 | 15 | 93301416 | 93301647 | - | pseudogenic_transcript | processed_pseudogene |
| 245700 | enst00000543286 | sg00000257060 | ac091078.1-202 | 15 | 93312557 | 93554870 | + | lnc_RNA | lncrna |
| 245700 | enst00000554466 | sg00000257060 | ac091078.1-201 | 15 | 93312557 | 93530262 | + | lnc_RNA | lncrna |
| -246202 | enst00000610332 | sg00000272888 | linc01578-210 | 15 | 92819598 | 92819992 | + | lnc_RNA | lncrna |
| 246245 | enst00000554105 | sg00000257060 | ac091078.1-203 | 15 | 93313102 | 93554871 | + | lnc_RNA | lncrna |
| -246260 | enst00000653163 | sg00000272888 | linc01578-211 | 15 | 92819540 | 92898743 | + | lnc_RNA | lncrna |
| 246262 | enst00000657519 | sg00000257060 | ac091078.1-206 | 15 | 93313119 | 93499194 | + | lnc_RNA | lncrna |
| 246321 | enst00000653095 | sg00000257060 | ac091078.1-207 | 15 | 93313178 | 93498903 | + | lnc_RNA | lncrna |
| 246329 | enst00000556519 | sg00000257060 | ac091078.1-204 | 15 | 93313186 | 93499453 | + | lnc_RNA | lncrna |
| 246349 | enst00000553478 | sg00000257060 | ac091078.1-205 | 15 | 93313206 | 93569483 | + | lnc_RNA | lncrna |
| 246388 | enst00000668028 | sg00000257060 | ac091078.1-209 | 15 | 93313245 | 93499333 | + | lnc_RNA | lncrna |
| 246394 | enst00000657206 | sg00000257060 | ac091078.1-208 | 15 | 93313251 | 93554868 | + | lnc_RNA | lncrna |
| 246394 | enst00000667940 | sg00000257060 | ac091078.1-213 | 15 | 93313251 | 93499195 | + | lnc_RNA | lncrna |
| 255390 | enst00000654088 | sg00000257060 | ac091078.1-210 | 15 | 93322247 | 93499198 | + | lnc_RNA | lncrna |
| -255916 | enst00000554082 | sg00000185442 | fam174b-203 | 15 | 92808844 | 92809884 | - | lnc_RNA | processed_transcript |
| -255939 | enst00000555971 | sg00000185442 | fam174b-208 | 15 | 92782055 | 92809861 | - | lnc_RNA | processed_transcript |
| -256002 | enst00000557398 | sg00000185442 | fam174b-210 | 15 | 92619302 | 92809798 | - | mRNA | protein_coding |
| -257233 | enst00000555325 | sg00000258922 | ac106028.2-201 | 15 | 92805770 | 92808567 | - | lnc_RNA | lncrna |
| -257349 | enst00000614509 | sg00000274215 | ac106028.4-201 | 15 | 92808451 | 92809057 | + | lnc_RNA | lncrna |
| -270153 | enst00000557146 | sg00000258527 | asb9p1-201 | 15 | 92795647 | 92796439 | + | pseudogenic_transcript | processed_pseudogene |
| -277328 | enst00000557545 | sg00000185442 | fam174b-212 | 15 | 92787914 | 92788472 | - | lnc_RNA | processed_transcript |
| -284308 | enst00000562894 | sg00000260361 | ac106028.3-201 | 15 | 92779757 | 92781492 | - | lnc_RNA | lncrna |
| -303043 | enst00000554322 | sg00000258562 | ac106028.1-201 | 15 | 92762757 | 92763750 | + | pseudogenic_transcript | processed_pseudogene |
| -331595 | enst00000671695 | sg00000258741 | h2az2p1-203 | 15 | 92713477 | 92734205 | - | lnc_RNA | processed_transcript |
| -331605 | enst00000554246 | sg00000258741 | h2az2p1-201 | 15 | 92733823 | 92734195 | - | pseudogenic_transcript | transcribed_processed_pseudogene |
| -331702 | enst00000556424 | sg00000258741 | h2az2p1-202 | 15 | 92715710 | 92734098 | - | lnc_RNA | processed_transcript |
| -341523 | enst00000554000 | sg00000272298 | ac091544.6-201 | 15 | 92699040 | 92724277 | - | lnc_RNA | lncrna |
| -346407 | enst00000484702 | sg00000240484 | ac091544.1-201 | 15 | 92719393 | 92719740 | + | pseudogenic_transcript | processed_pseudogene |
| -353992 | enst00000431116 | sg00000253954 | hmgn1p38-201 | 15 | 92711808 | 92712110 | + | pseudogenic_transcript | processed_pseudogene |
| 355719 | enst00000556708 | sg00000258909 | ac091078.2-201 | 15 | 93416850 | 93422576 | - | lnc_RNA | lncrna |
| 364360 | enst00000557145 | sg00000258787 | sephs1p2-201 | 15 | 93430659 | 93431217 | - | pseudogenic_transcript | processed_pseudogene |
| 388124 | enst00000661485 | sg00000257060 | ac091078.1-212 | 15 | 93454981 | 93499335 | + | lnc_RNA | lncrna |
| -397757 | enst00000557480 | sg00000185442 | fam174b-211 | 15 | 92619183 | 92668043 | - | mRNA | protein_coding |
| -409169 | enst00000556824 | sg00000185442 | fam174b-209 | 15 | 92619238 | 92656631 | - | mRNA | protein_coding |
| -410025 | enst00000327355 | sg00000185442 | fam174b-201 | 15 | 92617448 | 92655775 | - | mRNA | protein_coding |
| -410396 | enst00000555748 | sg00000185442 | fam174b-207 | 15 | 92619000 | 92655404 | - | mRNA | protein_coding |
| -410449 | enst00000555613 | sg00000185442 | fam174b-205 | 15 | 92630161 | 92655351 | - | lnc_RNA | retained_intron |
| -412590 | enst00000555696 | sg00000185442 | fam174b-206 | 15 | 92619119 | 92653210 | - | mRNA | protein_coding |
| -420202 | enst00000553393 | sg00000185442 | fam174b-202 | 15 | 92617448 | 92645598 | - | mRNA | protein_coding |
| -426556 | enst00000555064 | sg00000185442 | fam174b-204 | 15 | 92619058 | 92639244 | - | mRNA | protein_coding |
| -431495 | enst00000619490 | sg00000275965 | ac091544.7-201 | 15 | 92634305 | 92634665 | + | lnc_RNA | lncrna |
| -438727 | enst00000555268 | sg00000259064 | ac091544.3-201 | 15 | 92627073 | 92627414 | + | pseudogenic_transcript | processed_pseudogene |
| -462890 | enst00000607766 | sg00000271763 | ac091544.5-201 | 15 | 92602910 | 92620015 | + | lnc_RNA | lncrna |
| -467242 | enst00000625146 | sg00000258676 | ac091544.2-202 | 15 | 92598558 | 92600537 | + | unconfirmed_transcript | tec |
| -469338 | enst00000568297 | sg00000260337 | ac091544.4-204 | 15 | 92595560 | 92596462 | - | lnc_RNA | lncrna |
| -469412 | enst00000620192 | sg00000260337 | ac091544.4-201 | 15 | 92592574 | 92596388 | - | lnc_RNA | lncrna |
| -469489 | enst00000654742 | sg00000260337 | ac091544.4-202 | 15 | 92592593 | 92596311 | - | lnc_RNA | lncrna |
| -469839 | enst00000658288 | sg00000260337 | ac091544.4-203 | 15 | 92593020 | 92595961 | - | lnc_RNA | lncrna |
| -474234 | enst00000670432 | sg00000258676 | ac091544.2-203 | 15 | 92591566 | 92600542 | + | lnc_RNA | lncrna |
| -474259 | enst00000665942 | sg00000258676 | ac091544.2-204 | 15 | 92591541 | 92594043 | + | lnc_RNA | lncrna |
| -474276 | enst00000671549 | sg00000258676 | ac091544.2-206 | 15 | 92591524 | 92600545 | + | lnc_RNA | lncrna |
| -484981 | enst00000555864 | sg00000258676 | ac091544.2-201 | 15 | 92580819 | 92600545 | + | lnc_RNA | lncrna |
| -485059 | enst00000654959 | sg00000258676 | ac091544.2-205 | 15 | 92580741 | 92581675 | + | lnc_RNA | lncrna |
| -491271 | enst00000654017 | sg00000258647 | linc00930-204 | 15 | 92567817 | 92574529 | - | lnc_RNA | lncrna |
| -491281 | enst00000653070 | sg00000258647 | linc00930-203 | 15 | 92567817 | 92574519 | - | lnc_RNA | lncrna |
| -491283 | enst00000554542 | sg00000258647 | linc00930-201 | 15 | 92567819 | 92574517 | - | lnc_RNA | lncrna |
| -494103 | enst00000557075 | sg00000258647 | linc00930-202 | 15 | 92567820 | 92571697 | - | lnc_RNA | lncrna |
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