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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 |
|---|---|---|---|---|---|---|---|---|
| #165 | 6 | 35317842 | 35318953 | 1111 | 3 | 33 | 5.73929e-15 | 3.45922e-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 |
|---|---|---|---|---|---|---|---|---|---|
| -234 | enst00000468102 | sg00000023892 | def6-203 | 6 | 35317608 | 35318230 | + | lnc_RNA | processed_transcript |
| -8104 | enst00000444278 | sg00000023892 | def6-202 | 6 | 35309738 | 35312538 | + | mRNA | protein_coding |
| -20024 | enst00000316637 | sg00000023892 | def6-201 | 6 | 35297818 | 35321771 | + | mRNA | protein_coding |
| 23605 | enst00000448077 | sg00000112033 | ppard-205 | 6 | 35342558 | 35428191 | + | mRNA | protein_coding |
| 23605 | enst00000418635 | sg00000112033 | ppard-204 | 6 | 35342558 | 35428191 | + | mRNA | protein_coding |
| 23605 | enst00000360694 | sg00000112033 | ppard-203 | 6 | 35342558 | 35428178 | + | mRNA | protein_coding |
| 23661 | enst00000311565 | sg00000112033 | ppard-201 | 6 | 35342614 | 35428178 | + | mRNA | protein_coding |
| 23661 | enst00000337400 | sg00000112033 | ppard-202 | 6 | 35342614 | 35425393 | + | mRNA | protein_coding |
| -24018 | enst00000498555 | sg00000065029 | znf76-211 | 6 | 35293824 | 35294976 | + | mRNA | protein_coding |
| -25519 | enst00000479226 | sg00000065029 | znf76-206 | 6 | 35292323 | 35294552 | + | lnc_RNA | retained_intron |
| -38023 | enst00000402490 | sg00000217004 | z97832.1-201 | 6 | 35279177 | 35279819 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -47430 | enst00000482946 | sg00000065029 | znf76-207 | 6 | 35270412 | 35281105 | + | lnc_RNA | processed_transcript |
| -58068 | enst00000339411 | sg00000065029 | znf76-202 | 6 | 35259774 | 35295983 | + | mRNA | protein_coding |
| -58107 | enst00000373953 | sg00000065029 | znf76-203 | 6 | 35259735 | 35295985 | + | mRNA | protein_coding |
| -58238 | enst00000460229 | sg00000065029 | znf76-204 | 6 | 35259604 | 35287777 | + | lnc_RNA | retained_intron |
| -58314 | enst00000484932 | sg00000065029 | znf76-208 | 6 | 35259528 | 35286782 | + | lnc_RNA | retained_intron |
| -58344 | enst00000486891 | sg00000065029 | znf76-209 | 6 | 35259498 | 35292134 | + | lnc_RNA | retained_intron |
| -58371 | enst00000469195 | sg00000065029 | znf76-205 | 6 | 35259471 | 35292642 | + | mRNA | protein_coding |
| -58860 | enst00000229405 | sg00000065029 | znf76-201 | 6 | 35258982 | 35295983 | + | mRNA | nonsense_mediated_decay |
| -58933 | enst00000491400 | sg00000065029 | znf76-210 | 6 | 35258909 | 35288315 | + | lnc_RNA | retained_intron |
| -93212 | enst00000605896 | sg00000272374 | z97832.2-201 | 6 | 35220370 | 35224630 | - | lnc_RNA | lncrna |
| -103886 | enst00000274938 | sg00000146197 | scube3-201 | 6 | 35213956 | 35253079 | + | mRNA | protein_coding |
| 124091 | enst00000436521 | sg00000227154 | al022721.1-201 | 6 | 35443044 | 35449847 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 133385 | enst00000229769 | sg00000112039 | fance-201 | 6 | 35452338 | 35467102 | + | mRNA | protein_coding |
| 133403 | enst00000648059 | sg00000112039 | fance-202 | 6 | 35452356 | 35466961 | + | mRNA | nonsense_mediated_decay |
| 149448 | enst00000322203 | sg00000198755 | rpl10a-201 | 6 | 35468401 | 35470780 | + | mRNA | protein_coding |
| 149455 | enst00000467020 | sg00000198755 | rpl10a-203 | 6 | 35468408 | 35470785 | + | lnc_RNA | processed_transcript |
| 149467 | enst00000478340 | sg00000198755 | rpl10a-204 | 6 | 35468420 | 35470785 | + | lnc_RNA | processed_transcript |
| 149467 | enst00000490335 | sg00000198755 | rpl10a-205 | 6 | 35468420 | 35470640 | + | lnc_RNA | processed_transcript |
| 149467 | enst00000464112 | sg00000198755 | rpl10a-202 | 6 | 35468420 | 35470785 | + | lnc_RNA | processed_transcript |
| 151555 | enst00000619751 | sg00000276712 | mir7111-201 | 6 | 35470508 | 35470579 | + | miRNA | mirna |
| -169232 | enst00000418521 | sg00000124678 | tcp11-207 | 6 | 35118269 | 35148610 | - | mRNA | protein_coding |
| -176432 | enst00000611141 | sg00000124678 | tcp11-228 | 6 | 35118077 | 35141410 | - | mRNA | protein_coding |
| -176432 | enst00000673754 | sg00000124678 | tcp11-229 | 6 | 35118077 | 35141410 | - | mRNA | protein_coding |
| -176432 | enst00000244645 | sg00000124678 | tcp11-201 | 6 | 35118077 | 35141410 | - | mRNA | protein_coding |
| -176471 | enst00000373974 | sg00000124678 | tcp11-203 | 6 | 35118135 | 35141371 | - | mRNA | protein_coding |
| -176489 | enst00000427376 | sg00000124678 | tcp11-208 | 6 | 35119240 | 35141353 | - | mRNA | nonsense_mediated_decay |
| -176489 | enst00000492680 | sg00000124678 | tcp11-215 | 6 | 35122199 | 35141353 | - | mRNA | protein_coding |
| -176493 | enst00000455706 | sg00000124678 | tcp11-211 | 6 | 35118072 | 35141349 | - | mRNA | nonsense_mediated_decay |
| -176503 | enst00000469514 | sg00000124678 | tcp11-212 | 6 | 35120429 | 35141339 | - | mRNA | nonsense_mediated_decay |
| -176503 | enst00000311875 | sg00000124678 | tcp11-202 | 6 | 35118075 | 35141339 | - | mRNA | protein_coding |
| -176503 | enst00000444780 | sg00000124678 | tcp11-209 | 6 | 35118074 | 35141339 | - | mRNA | protein_coding |
| -176506 | enst00000507706 | sg00000124678 | tcp11-223 | 6 | 35122252 | 35141336 | - | mRNA | protein_coding |
| -176506 | enst00000373979 | sg00000124678 | tcp11-204 | 6 | 35118071 | 35141336 | - | mRNA | protein_coding |
| -176519 | enst00000412155 | sg00000124678 | tcp11-206 | 6 | 35118071 | 35141323 | - | mRNA | protein_coding |
| -176526 | enst00000505335 | sg00000124678 | tcp11-220 | 6 | 35122309 | 35141316 | - | mRNA | nonsense_mediated_decay |
| -176529 | enst00000394696 | sg00000124678 | tcp11-205 | 6 | 35128705 | 35141313 | - | lnc_RNA | processed_transcript |
| -176529 | enst00000510465 | sg00000124678 | tcp11-225 | 6 | 35128689 | 35141313 | - | lnc_RNA | processed_transcript |
| -176529 | enst00000445851 | sg00000124678 | tcp11-210 | 6 | 35128358 | 35141313 | - | lnc_RNA | processed_transcript |
| -176529 | enst00000505400 | sg00000124678 | tcp11-221 | 6 | 35122297 | 35141313 | - | mRNA | protein_coding |
| -176531 | enst00000503908 | sg00000124678 | tcp11-218 | 6 | 35129115 | 35141311 | - | mRNA | nonsense_mediated_decay |
| -176531 | enst00000509988 | sg00000124678 | tcp11-224 | 6 | 35122305 | 35141311 | - | mRNA | nonsense_mediated_decay |
| -176531 | enst00000514751 | sg00000124678 | tcp11-227 | 6 | 35137746 | 35141311 | - | mRNA | nonsense_mediated_decay |
| -176532 | enst00000486638 | sg00000124678 | tcp11-214 | 6 | 35120186 | 35141310 | - | mRNA | protein_coding |
| -176578 | enst00000479418 | sg00000124678 | tcp11-213 | 6 | 35122286 | 35141264 | - | mRNA | nonsense_mediated_decay |
| -176578 | enst00000505911 | sg00000124678 | tcp11-222 | 6 | 35118072 | 35141264 | - | mRNA | nonsense_mediated_decay |
| -176589 | enst00000504758 | sg00000124678 | tcp11-219 | 6 | 35118072 | 35141253 | - | mRNA | nonsense_mediated_decay |
| -176613 | enst00000673967 | sg00000124678 | tcp11-230 | 6 | 35118269 | 35141229 | - | mRNA | protein_coding |
| -176815 | enst00000512012 | sg00000124678 | tcp11-226 | 6 | 35118269 | 35141027 | - | mRNA | protein_coding |
| -176815 | enst00000503195 | sg00000124678 | tcp11-217 | 6 | 35136127 | 35141027 | - | mRNA | nonsense_mediated_decay |
| 177997 | enst00000402886 | sg00000007866 | tead3-202 | 6 | 35473597 | 35496950 | - | mRNA | nonsense_mediated_decay |
| 178111 | enst00000639578 | sg00000007866 | tead3-203 | 6 | 35474892 | 35497064 | - | mRNA | protein_coding |
| 178126 | enst00000338863 | sg00000007866 | tead3-201 | 6 | 35473597 | 35497079 | - | mRNA | protein_coding |
| 185183 | enst00000495781 | sg00000112041 | tulp1-206 | 6 | 35500070 | 35504136 | - | lnc_RNA | retained_intron |
| 187065 | enst00000496434 | sg00000112041 | tulp1-207 | 6 | 35503386 | 35506018 | - | lnc_RNA | retained_intron |
| 193014 | enst00000373892 | sg00000112041 | tulp1-203 | 6 | 35503751 | 35511967 | - | lnc_RNA | retained_intron |
| 193321 | enst00000448446 | sg00000112041 | tulp1-205 | 6 | 35510706 | 35512274 | - | lnc_RNA | retained_intron |
| 193913 | enst00000428978 | sg00000112041 | tulp1-204 | 6 | 35509724 | 35512866 | - | mRNA | protein_coding |
| 193916 | enst00000614066 | sg00000112041 | tulp1-208 | 6 | 35497877 | 35512869 | - | mRNA | protein_coding |
| 193923 | enst00000322263 | sg00000112041 | tulp1-202 | 6 | 35497874 | 35512876 | - | mRNA | protein_coding |
| 193943 | enst00000229771 | sg00000112041 | tulp1-201 | 6 | 35497874 | 35512896 | - | mRNA | protein_coding |
| -196797 | enst00000502480 | sg00000124678 | tcp11-216 | 6 | 35118072 | 35121045 | - | mRNA | protein_coding |
| 220885 | enst00000664260 | sg00000228559 | al033519.4-203 | 6 | 35539838 | 35545671 | + | lnc_RNA | lncrna |
| 224777 | enst00000658088 | sg00000228559 | al033519.4-202 | 6 | 35543730 | 35546573 | + | lnc_RNA | lncrna |
| 225679 | enst00000450618 | sg00000228559 | al033519.4-201 | 6 | 35544632 | 35545669 | + | lnc_RNA | lncrna |
| 236920 | enst00000403958 | sg00000219023 | al033519.3-201 | 6 | 35555873 | 35556264 | + | pseudogenic_transcript | processed_pseudogene |
| -246793 | enst00000616756 | sg00000273870 | al138721.1-201 | 6 | 35070871 | 35071049 | - | pseudogenic_transcript | processed_pseudogene |
| -259594 | enst00000470698 | sg00000064999 | anks1a-202 | 6 | 35058248 | 35081053 | + | lnc_RNA | processed_transcript |
| -259827 | enst00000660796 | sg00000286550 | al591002.1-201 | 6 | 35041116 | 35058015 | - | lnc_RNA | lncrna |
| 288675 | enst00000407266 | sg00000218749 | al033519.2-201 | 6 | 35607628 | 35607934 | + | pseudogenic_transcript | processed_pseudogene |
| -294320 | enst00000339579 | sg00000187762 | hspe1p11-201 | 6 | 35023522 | 35023831 | + | pseudogenic_transcript | processed_pseudogene |
| 332044 | enst00000659695 | sg00000287458 | al033519.5-201 | 6 | 35650997 | 35652856 | + | lnc_RNA | lncrna |
| 332865 | enst00000391277 | sg00000212579 | al033519.1-201 | 6 | 35651818 | 35651945 | + | snoRNA | snorna |
| 345836 | enst00000583739 | sg00000265527 | mir5690-201 | 6 | 35664717 | 35664789 | - | miRNA | mirna |
| 369962 | enst00000539068 | sg00000096060 | fkbp5-203 | 6 | 35573585 | 35688915 | - | mRNA | protein_coding |
| 369984 | enst00000357266 | sg00000096060 | fkbp5-201 | 6 | 35573590 | 35688937 | - | mRNA | protein_coding |
| 369989 | enst00000542713 | sg00000096060 | fkbp5-204 | 6 | 35580557 | 35688942 | - | mRNA | protein_coding |
| 409630 | enst00000536438 | sg00000096060 | fkbp5-202 | 6 | 35573585 | 35728583 | - | mRNA | protein_coding |
| 417994 | enst00000452048 | sg00000232909 | al157823.2-201 | 6 | 35733867 | 35736947 | - | lnc_RNA | lncrna |
| 418079 | enst00000373869 | sg00000157343 | armc12-203 | 6 | 35737032 | 35748911 | + | mRNA | protein_coding |
| 418129 | enst00000288065 | sg00000157343 | armc12-201 | 6 | 35737082 | 35748908 | + | mRNA | protein_coding |
| 418134 | enst00000373866 | sg00000157343 | armc12-202 | 6 | 35737087 | 35749079 | + | mRNA | protein_coding |
| 418139 | enst00000471400 | sg00000157343 | armc12-204 | 6 | 35737092 | 35738509 | + | mRNA | nonsense_mediated_decay |
| -428528 | enst00000650178 | sg00000064999 | anks1a-204 | 6 | 34889314 | 34989316 | + | mRNA | protein_coding |
| -428577 | enst00000649117 | sg00000064999 | anks1a-203 | 6 | 34889265 | 35088963 | + | mRNA | protein_coding |
| -428587 | enst00000360359 | sg00000064999 | anks1a-201 | 6 | 34889255 | 35091406 | + | mRNA | protein_coding |
| -429771 | enst00000420584 | sg00000064995 | taf11-202 | 6 | 34877778 | 34888071 | - | mRNA | protein_coding |
| -429800 | enst00000361288 | sg00000064995 | taf11-201 | 6 | 34877462 | 34888042 | - | mRNA | protein_coding |
| -429815 | enst00000650109 | sg00000064995 | taf11-203 | 6 | 34877462 | 34888027 | - | mRNA | protein_coding |
| -444011 | enst00000516297 | sg00000252106 | rny3p15-201 | 6 | 34873831 | 34873927 | + | ncRNA | misc_rna |
| 446955 | enst00000403727 | sg00000220734 | al157823.1-201 | 6 | 35765908 | 35766927 | + | pseudogenic_transcript | processed_pseudogene |
| 457641 | enst00000481904 | sg00000196748 | clpsl2-204 | 6 | 35776594 | 35779552 | + | lnc_RNA | processed_transcript |
| 457645 | enst00000403376 | sg00000196748 | clpsl2-202 | 6 | 35776598 | 35779552 | + | mRNA | protein_coding |
| 457662 | enst00000360454 | sg00000196748 | clpsl2-201 | 6 | 35776615 | 35779552 | + | mRNA | protein_coding |
| 457737 | enst00000467122 | sg00000196748 | clpsl2-203 | 6 | 35776690 | 35779552 | + | lnc_RNA | processed_transcript |
| 462066 | enst00000373861 | sg00000204140 | clpsl1-201 | 6 | 35781019 | 35788150 | + | mRNA | protein_coding |
| 468087 | enst00000428710 | sg00000204140 | clpsl1-202 | 6 | 35787040 | 35793675 | + | mRNA | protein_coding |
| 477897 | enst00000622413 | sg00000137392 | clps-203 | 6 | 35794982 | 35796850 | - | mRNA | protein_coding |
| 478253 | enst00000651132 | sg00000197753 | lhfpl5-203 | 6 | 35797206 | 35824041 | + | mRNA | protein_coding |
| 478370 | enst00000259938 | sg00000137392 | clps-201 | 6 | 35794982 | 35797323 | - | mRNA | protein_coding |
| 478391 | enst00000616014 | sg00000137392 | clps-202 | 6 | 35794982 | 35797344 | - | mRNA | protein_coding |
| 486377 | enst00000651994 | sg00000197753 | lhfpl5-205 | 6 | 35805330 | 35823865 | + | mRNA | nonsense_mediated_decay |
| 486399 | enst00000360215 | sg00000197753 | lhfpl5-201 | 6 | 35805352 | 35824070 | + | mRNA | protein_coding |
| 486546 | enst00000651676 | sg00000197753 | lhfpl5-204 | 6 | 35805499 | 35845397 | + | mRNA | protein_coding |
| 486886 | enst00000652718 | sg00000197753 | lhfpl5-206 | 6 | 35805839 | 35837129 | + | mRNA | protein_coding |
| 492292 | enst00000496656 | sg00000197753 | lhfpl5-202 | 6 | 35811245 | 35833874 | + | lnc_RNA | processed_transcript |
| -496397 | enst00000383990 | sg00000206717 | al139100.1-201 | 6 | 34821445 | 34821542 | + | ncRNA | misc_rna |
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