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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 |
|---|---|---|---|---|---|---|---|---|
| #184 | 15 | 28454584 | 28455597 | 1013 | 3 | 34 | 1.9832e-14 | 1.07407e-12 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 2186 | enst00000564639 | sg00000260159 | ac091304.2-201 | 15 | 28454660 | 28457783 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -10440 | enst00000641554 | sg00000284628 | ac091304.10-201 | 15 | 28444144 | 28444264 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 17851 | enst00000563970 | sg00000261365 | ac138749.4-201 | 15 | 28473322 | 28473448 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -28093 | enst00000583920 | sg00000266039 | mir4509-2-201 | 15 | 28426491 | 28426584 | + | miRNA | mirna |
| -32412 | enst00000619761 | sg00000274532 | ac091304.6-201 | 15 | 28422172 | 28422373 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 35248 | enst00000578671 | sg00000263964 | mir4509-3-201 | 15 | 28490752 | 28490845 | - | miRNA | mirna |
| -38135 | enst00000612091 | sg00000276928 | ac091304.9-201 | 15 | 28416449 | 28416674 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 39585 | enst00000611461 | sg00000274814 | ac138749.5-201 | 15 | 28494975 | 28495182 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -51716 | enst00000561950 | sg00000261524 | abcb10p3-201 | 15 | 28402868 | 28405033 | + | pseudogenic_transcript | processed_pseudogene |
| 53211 | enst00000566803 | sg00000260053 | abcb10p4-201 | 15 | 28506625 | 28508808 | - | pseudogenic_transcript | processed_pseudogene |
| -67388 | enst00000613832 | sg00000276891 | rn7sl238p-201 | 15 | 28387196 | 28387485 | + | ncRNA | misc_rna |
| 68843 | enst00000616096 | sg00000276955 | ac138749.9-201 | 15 | 28524151 | 28524440 | - | ncRNA | misc_rna |
| 74815 | enst00000569308 | sg00000183629 | golga8g-207 | 15 | 28520763 | 28530412 | - | lnc_RNA | retained_intron |
| -75180 | enst00000568913 | sg00000153684 | golga8f-206 | 15 | 28379404 | 28382506 | + | lnc_RNA | retained_intron |
| -75920 | enst00000532622 | sg00000153684 | golga8f-202 | 15 | 28378664 | 28391224 | + | mRNA | protein_coding |
| -75920 | enst00000565126 | sg00000153684 | golga8f-204 | 15 | 28378664 | 28381453 | + | lnc_RNA | retained_intron |
| -75920 | enst00000526619 | sg00000153684 | golga8f-201 | 15 | 28378664 | 28392018 | + | mRNA | protein_coding |
| -75940 | enst00000568250 | sg00000153684 | golga8f-205 | 15 | 28378644 | 28383063 | + | lnc_RNA | retained_intron |
| -75963 | enst00000564114 | sg00000153684 | golga8f-203 | 15 | 28378621 | 28382542 | + | lnc_RNA | retained_intron |
| 76627 | enst00000570018 | sg00000183629 | golga8g-208 | 15 | 28529129 | 28532224 | - | lnc_RNA | retained_intron |
| 77373 | enst00000562627 | sg00000183629 | golga8g-205 | 15 | 28519615 | 28532970 | - | lnc_RNA | retained_intron |
| 77374 | enst00000524859 | sg00000183629 | golga8g-202 | 15 | 28519615 | 28532971 | - | lnc_RNA | retained_intron |
| 77374 | enst00000525590 | sg00000183629 | golga8g-203 | 15 | 28522573 | 28532971 | - | mRNA | protein_coding |
| 77374 | enst00000568534 | sg00000183629 | golga8g-206 | 15 | 28530182 | 28532971 | - | lnc_RNA | retained_intron |
| 77374 | enst00000382949 | sg00000183629 | golga8g-201 | 15 | 28519611 | 28532971 | - | lnc_RNA | retained_intron |
| 77417 | enst00000561497 | sg00000183629 | golga8g-204 | 15 | 28529002 | 28533014 | - | lnc_RNA | retained_intron |
| -88853 | enst00000565703 | sg00000261497 | ac091304.4-201 | 15 | 28362796 | 28365731 | - | pseudogenic_transcript | unprocessed_pseudogene |
| 90315 | enst00000567691 | sg00000261041 | ac138749.3-201 | 15 | 28545912 | 28549777 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -96504 | enst00000568624 | sg00000237850 | ac091304.1-202 | 15 | 28349051 | 28358080 | - | lnc_RNA | processed_transcript |
| -96570 | enst00000564897 | sg00000237850 | ac091304.1-201 | 15 | 28349051 | 28358014 | - | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 98041 | enst00000567652 | sg00000227717 | ac138749.1-201 | 15 | 28553638 | 28561379 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -108094 | enst00000568969 | sg00000261561 | ac091304.5-201 | 15 | 28346490 | 28346647 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 109555 | enst00000566048 | sg00000260444 | ac138749.2-201 | 15 | 28564986 | 28565152 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -122347 | enst00000566500 | sg00000261401 | ac091304.3-201 | 15 | 28332237 | 28336609 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 123803 | enst00000562845 | sg00000261581 | herc2p11-201 | 15 | 28575019 | 28579400 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -132412 | enst00000261609 | sg00000128731 | herc2-201 | 15 | 28111040 | 28322172 | - | mRNA | protein_coding |
| -132435 | enst00000564734 | sg00000128731 | herc2-207 | 15 | 28254488 | 28322149 | - | mRNA | nonsense_mediated_decay |
| -132465 | enst00000563945 | sg00000128731 | herc2-204 | 15 | 28320122 | 28322119 | - | lnc_RNA | processed_transcript |
| 133895 | enst00000507787 | sg00000206149 | herc2p9-201 | 15 | 28589492 | 28591123 | + | lnc_RNA | retained_intron |
| 134592 | enst00000529624 | sg00000206149 | herc2p9-206 | 15 | 28590189 | 28674027 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -138933 | enst00000544920 | sg00000256338 | rpl41p2-201 | 15 | 28315651 | 28316059 | + | pseudogenic_transcript | processed_pseudogene |
| -155101 | enst00000564383 | sg00000128731 | herc2-205 | 15 | 28280034 | 28299483 | - | lnc_RNA | retained_intron |
| 156545 | enst00000529537 | sg00000206149 | herc2p9-205 | 15 | 28612142 | 28633274 | + | lnc_RNA | processed_transcript |
| 177526 | enst00000524476 | sg00000206149 | herc2p9-202 | 15 | 28633123 | 28641565 | + | lnc_RNA | retained_intron |
| 177528 | enst00000529353 | sg00000206149 | herc2p9-204 | 15 | 28633125 | 28642421 | + | lnc_RNA | processed_transcript |
| -181416 | enst00000563670 | sg00000128731 | herc2-203 | 15 | 28272044 | 28273168 | - | lnc_RNA | retained_intron |
| 195824 | enst00000530420 | sg00000206149 | herc2p9-207 | 15 | 28651421 | 28673915 | + | lnc_RNA | retained_intron |
| 198845 | enst00000528584 | sg00000206149 | herc2p9-203 | 15 | 28654442 | 28685264 | + | lnc_RNA | processed_transcript |
| 216238 | enst00000569226 | sg00000206149 | herc2p9-208 | 15 | 28671835 | 28682178 | + | lnc_RNA | retained_intron |
| -225068 | enst00000569335 | sg00000128731 | herc2-211 | 15 | 28222148 | 28229516 | - | lnc_RNA | retained_intron |
| 226655 | enst00000531834 | sg00000254398 | ac055876.2-201 | 15 | 28679405 | 28682252 | - | pseudogenic_transcript | unprocessed_pseudogene |
| 248193 | enst00000620196 | sg00000274632 | rn7sl719p-201 | 15 | 28703554 | 28703790 | - | ncRNA | misc_rna |
| -250648 | enst00000567869 | sg00000128731 | herc2-209 | 15 | 28190201 | 28203936 | - | lnc_RNA | retained_intron |
| 256726 | enst00000563027 | sg00000188626 | golga8m-201 | 15 | 28701954 | 28712323 | - | mRNA | protein_coding |
| -262462 | enst00000650509 | sg00000128731 | herc2-214 | 15 | 28111079 | 28192122 | - | mRNA | nonsense_mediated_decay |
| -280161 | enst00000569772 | sg00000128731 | herc2-212 | 15 | 28152759 | 28174423 | - | mRNA | protein_coding |
| 281986 | enst00000563942 | sg00000248334 | whammp2-203 | 15 | 28737583 | 28754869 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 282425 | enst00000515318 | sg00000248334 | whammp2-202 | 15 | 28738022 | 28748426 | + | lnc_RNA | retained_intron |
| 282787 | enst00000563213 | sg00000188626 | golga8m-202 | 15 | 28709267 | 28738384 | - | lnc_RNA | processed_transcript |
| 282834 | enst00000568033 | sg00000261480 | golga8m-203 | 15 | 28719377 | 28738431 | - | lnc_RNA | lncrna |
| 285504 | enst00000512149 | sg00000248334 | whammp2-201 | 15 | 28741101 | 28759204 | + | lnc_RNA | processed_transcript |
| 308554 | enst00000562515 | sg00000260844 | ac055876.4-201 | 15 | 28763440 | 28764151 | - | pseudogenic_transcript | processed_pseudogene |
| -312132 | enst00000564519 | sg00000128731 | herc2-206 | 15 | 28141739 | 28142452 | - | lnc_RNA | retained_intron |
| -319028 | enst00000649023 | sg00000128731 | herc2-213 | 15 | 28130300 | 28135556 | - | lnc_RNA | processed_transcript |
| 332646 | enst00000430589 | sg00000232431 | ac055876.1-201 | 15 | 28788243 | 28789392 | + | lnc_RNA | processed_transcript |
| 333005 | enst00000567053 | sg00000232431 | ac055876.1-202 | 15 | 28788602 | 28792002 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 333602 | enst00000431496 | sg00000256951 | ac055876.3-201 | 15 | 28789199 | 28789486 | + | pseudogenic_transcript | transcribed_processed_pseudogene |
| 334067 | enst00000565892 | sg00000261377 | pdcd6ipp2-205 | 15 | 28789664 | 28790304 | + | lnc_RNA | processed_transcript |
| 334230 | enst00000562423 | sg00000261377 | pdcd6ipp2-201 | 15 | 28789827 | 28808298 | + | lnc_RNA | processed_transcript |
| -336163 | enst00000568206 | sg00000128731 | herc2-210 | 15 | 28115281 | 28118421 | - | lnc_RNA | retained_intron |
| -337033 | enst00000566635 | sg00000128731 | herc2-208 | 15 | 28111279 | 28117551 | - | lnc_RNA | retained_intron |
| -340867 | enst00000562136 | sg00000128731 | herc2-202 | 15 | 28111762 | 28113717 | - | lnc_RNA | retained_intron |
| 345769 | enst00000566321 | sg00000261377 | pdcd6ipp2-207 | 15 | 28801366 | 28818999 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -355269 | enst00000354638 | sg00000104044 | oca2-202 | 15 | 27754875 | 28099315 | - | mRNA | protein_coding |
| -355272 | enst00000353809 | sg00000104044 | oca2-201 | 15 | 27754875 | 28099312 | - | mRNA | protein_coding |
| -355288 | enst00000445578 | sg00000104044 | oca2-204 | 15 | 28016104 | 28099296 | - | mRNA | protein_coding |
| -355291 | enst00000431101 | sg00000104044 | oca2-203 | 15 | 28018412 | 28099293 | - | mRNA | protein_coding |
| 359749 | enst00000563202 | sg00000261377 | pdcd6ipp2-203 | 15 | 28815346 | 28833337 | + | lnc_RNA | processed_transcript |
| 375585 | enst00000605667 | sg00000271616 | ac055876.5-201 | 15 | 28830619 | 28831182 | - | pseudogenic_transcript | processed_pseudogene |
| 376724 | enst00000566178 | sg00000261377 | pdcd6ipp2-206 | 15 | 28832321 | 28859007 | + | lnc_RNA | processed_transcript |
| 376734 | enst00000564604 | sg00000261377 | pdcd6ipp2-204 | 15 | 28832331 | 28851557 | + | lnc_RNA | processed_transcript |
| 376783 | enst00000563144 | sg00000261377 | pdcd6ipp2-202 | 15 | 28832380 | 28838983 | + | lnc_RNA | processed_transcript |
| 393078 | enst00000567390 | sg00000261649 | golga6l7-201 | 15 | 28841833 | 28848675 | - | mRNA | protein_coding |
| 393078 | enst00000569815 | sg00000261649 | golga6l7-202 | 15 | 28844961 | 28848675 | - | lnc_RNA | retained_intron |
| 402801 | enst00000603069 | sg00000270301 | ac174071.1-201 | 15 | 28857882 | 28858398 | - | pseudogenic_transcript | processed_pseudogene |
| 428886 | enst00000561069 | sg00000034053 | apba2-212 | 15 | 28884483 | 29117717 | + | mRNA | protein_coding |
| 429058 | enst00000669290 | sg00000287894 | ac174469.1-201 | 15 | 28881667 | 28884655 | - | lnc_RNA | lncrna |
| 430377 | enst00000558402 | sg00000034053 | apba2-207 | 15 | 28885974 | 29118315 | + | mRNA | protein_coding |
| 430425 | enst00000558330 | sg00000034053 | apba2-205 | 15 | 28886022 | 29117717 | + | mRNA | protein_coding |
| 430563 | enst00000559814 | sg00000034053 | apba2-210 | 15 | 28886160 | 29108620 | + | lnc_RNA | retained_intron |
| 430566 | enst00000559709 | sg00000034053 | apba2-209 | 15 | 28886163 | 29053897 | + | mRNA | protein_coding |
| 463770 | enst00000558804 | sg00000034053 | apba2-208 | 15 | 28919367 | 29054094 | + | mRNA | protein_coding |
| 466040 | enst00000411764 | sg00000034053 | apba2-202 | 15 | 28921637 | 29118311 | + | mRNA | protein_coding |
| 466040 | enst00000558259 | sg00000034053 | apba2-204 | 15 | 28921637 | 29118311 | + | mRNA | protein_coding |
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