PycoMeth
Documentation
GitHub
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 |
|---|---|---|---|---|---|---|---|---|
| #169 | 6 | 27830671 | 27831771 | 1100 | 3 | 32 | 8.34645e-15 | 4.91156e-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 | enst00000611927 | sg00000273542 | h4c12-201 | 6 | 27831216 | 27831527 | - | mRNA | protein_coding |
| 5989 | enst00000612898 | sg00000233822 | h2bc15-204 | 6 | 27837760 | 27839482 | + | mRNA | protein_coding |
| -6563 | enst00000355057 | sg00000197238 | h4c11-201 | 6 | 27824108 | 27824480 | + | mRNA | protein_coding |
| 6568 | enst00000618958 | sg00000275221 | h2ac15-201 | 6 | 27837947 | 27838339 | - | mRNA | protein_coding |
| 6774 | enst00000449538 | sg00000233822 | h2bc15-202 | 6 | 27838545 | 27852204 | + | mRNA | nonsense_mediated_decay |
| 6830 | enst00000606613 | sg00000233822 | h2bc15-203 | 6 | 27838601 | 27855709 | + | mRNA | protein_coding |
| 6891 | enst00000396980 | sg00000233822 | h2bc15-201 | 6 | 27838662 | 27865798 | + | mRNA | protein_coding |
| -15627 | enst00000621112 | sg00000273703 | h2bc14-201 | 6 | 27815044 | 27815424 | + | mRNA | protein_coding |
| -15931 | enst00000333151 | sg00000276368 | h2ac14-201 | 6 | 27814354 | 27814740 | - | mRNA | protein_coding |
| -20607 | enst00000369163 | sg00000278828 | h3c10-201 | 6 | 27810064 | 27811300 | + | mRNA | protein_coding |
| -22472 | enst00000358739 | sg00000196747 | h2ac13-201 | 6 | 27808199 | 27808701 | + | mRNA | protein_coding |
| -22740 | enst00000377401 | sg00000185130 | h2bc13-201 | 6 | 27807444 | 27807931 | - | mRNA | protein_coding |
| -23596 | enst00000406085 | sg00000217862 | h4c10p-201 | 6 | 27807075 | 27807339 | + | pseudogenic_transcript | processed_pseudogene |
| 32630 | enst00000402707 | sg00000217646 | h2bc16p-201 | 6 | 27864062 | 27864401 | - | pseudogenic_transcript | processed_pseudogene |
| 33584 | enst00000613174 | sg00000276903 | h2ac16-201 | 6 | 27865355 | 27865747 | + | mRNA | protein_coding |
| 35758 | enst00000331442 | sg00000184357 | h1-5-201 | 6 | 27866849 | 27867529 | - | mRNA | protein_coding |
| 40544 | enst00000616365 | sg00000275379 | h3c11-201 | 6 | 27871905 | 27872315 | - | mRNA | protein_coding |
| 41739 | enst00000618305 | sg00000275126 | h4c13-201 | 6 | 27873199 | 27873510 | - | mRNA | protein_coding |
| -49560 | enst00000404972 | sg00000218069 | rsl24d1p1-201 | 6 | 27780619 | 27781111 | - | pseudogenic_transcript | processed_pseudogene |
| 59021 | enst00000359303 | sg00000197153 | h3c12-201 | 6 | 27890382 | 27890792 | - | mRNA | protein_coding |
| 61335 | enst00000479986 | sg00000197153 | h3c12-202 | 6 | 27890635 | 27893106 | - | lnc_RNA | processed_transcript |
| 61378 | enst00000359611 | sg00000278677 | h2ac17-201 | 6 | 27892757 | 27893149 | - | mRNA | protein_coding |
| 61692 | enst00000616182 | sg00000274641 | h2bc17-201 | 6 | 27893463 | 27893843 | + | mRNA | protein_coding |
| 65795 | enst00000458980 | sg00000238610 | rnu7-26p-201 | 6 | 27897504 | 27897566 | - | snRNA | snrna |
| -70801 | enst00000668543 | sg00000287252 | al009179.2-201 | 6 | 27759870 | 27763184 | + | lnc_RNA | lncrna |
| 80625 | enst00000303324 | sg00000168131 | or2b2-201 | 6 | 27911185 | 27912396 | - | mRNA | protein_coding |
| -92177 | enst00000407924 | sg00000216915 | gpr89p-201 | 6 | 27737000 | 27738494 | - | pseudogenic_transcript | processed_pseudogene |
| 105694 | enst00000439689 | sg00000168126 | or2w6p-201 | 6 | 27937465 | 27938403 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 125470 | enst00000244623 | sg00000124657 | or2b6-201 | 6 | 27957241 | 27958182 | + | mRNA | protein_coding |
| 133404 | enst00000398220 | sg00000214374 | rplp2p1-201 | 6 | 27965175 | 27965514 | + | pseudogenic_transcript | processed_pseudogene |
| -136230 | enst00000662411 | sg00000281706 | al009179.1-205 | 6 | 27694441 | 27713352 | + | lnc_RNA | lncrna |
| -136592 | enst00000629732 | sg00000281706 | al009179.1-204 | 6 | 27694079 | 27709157 | + | lnc_RNA | lncrna |
| -136598 | enst00000625477 | sg00000281706 | al009179.1-203 | 6 | 27694073 | 27702713 | + | lnc_RNA | lncrna |
| -136626 | enst00000628762 | sg00000281706 | al009179.1-202 | 6 | 27694045 | 27710222 | + | lnc_RNA | lncrna |
| -136636 | enst00000628328 | sg00000281706 | al009179.1-201 | 6 | 27694035 | 27711354 | + | lnc_RNA | lncrna |
| 145379 | enst00000406496 | sg00000216629 | or2w4p-201 | 6 | 27977150 | 27978075 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -150116 | enst00000668507 | sg00000287674 | al009179.3-201 | 6 | 27679971 | 27680555 | - | lnc_RNA | lncrna |
| -177846 | enst00000404273 | sg00000216676 | al031229.1-201 | 6 | 27652602 | 27652825 | - | pseudogenic_transcript | processed_pseudogene |
| 178952 | enst00000401788 | sg00000217539 | iqcb2p-201 | 6 | 28010723 | 28012355 | + | pseudogenic_transcript | processed_pseudogene |
| 183797 | enst00000362981 | sg00000199851 | al121944.1-201 | 6 | 28015568 | 28015777 | + | snoRNA | snorna |
| 202176 | enst00000406313 | sg00000217315 | or2w2p-201 | 6 | 28033947 | 28034855 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 214663 | enst00000429302 | sg00000187763 | or2b7p-201 | 6 | 28046434 | 28047367 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 222394 | enst00000432841 | sg00000182477 | or2b8p-201 | 6 | 28053228 | 28054165 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -234259 | enst00000383944 | sg00000206671 | rnu6-471p-201 | 6 | 27596412 | 27596517 | + | snRNA | snrna |
| 241545 | enst00000402365 | sg00000220721 | or1f12-201 | 6 | 28073316 | 28074260 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 248797 | enst00000377325 | sg00000197279 | znf165-201 | 6 | 28080568 | 28089563 | + | mRNA | protein_coding |
| 249359 | enst00000605945 | sg00000272009 | al121944.2-201 | 6 | 28078792 | 28081130 | - | lnc_RNA | lncrna |
| 259383 | enst00000529104 | sg00000219891 | zscan12p1-202 | 6 | 28091154 | 28093664 | + | lnc_RNA | processed_transcript |
| 260656 | enst00000406489 | sg00000219891 | zscan12p1-201 | 6 | 28092427 | 28092845 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -268927 | enst00000405625 | sg00000219738 | cd83p1-201 | 6 | 27560822 | 27561744 | - | pseudogenic_transcript | processed_pseudogene |
| 283857 | enst00000405929 | sg00000219392 | znf602p-201 | 6 | 28115628 | 28116551 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 292838 | enst00000340487 | sg00000196812 | zscan16-201 | 6 | 28124609 | 28130082 | + | mRNA | protein_coding |
| 305050 | enst00000660873 | sg00000269293 | zscan16-as1-203 | 6 | 28015122 | 28136821 | - | lnc_RNA | lncrna |
| 305073 | enst00000671586 | sg00000269293 | zscan16-as1-205 | 6 | 28136024 | 28136844 | - | lnc_RNA | lncrna |
| 305076 | enst00000667674 | sg00000269293 | zscan16-as1-204 | 6 | 28119782 | 28136847 | - | lnc_RNA | lncrna |
| 305078 | enst00000565046 | sg00000261839 | al358933.1-201 | 6 | 28136849 | 28139678 | + | lnc_RNA | lncrna |
| 305095 | enst00000602810 | sg00000269293 | zscan16-as1-202 | 6 | 28121798 | 28136866 | - | lnc_RNA | lncrna |
| 305522 | enst00000600652 | sg00000269293 | zscan16-as1-201 | 6 | 28121795 | 28137293 | - | lnc_RNA | lncrna |
| -307595 | enst00000401954 | sg00000218347 | hnrnpa1p1-201 | 6 | 27523076 | 27524339 | + | pseudogenic_transcript | processed_pseudogene |
| 310112 | enst00000330236 | sg00000198315 | zkscan8-201 | 6 | 28141883 | 28159460 | + | mRNA | protein_coding |
| 310139 | enst00000606198 | sg00000198315 | zkscan8-204 | 6 | 28141910 | 28154111 | + | mRNA | nonsense_mediated_decay |
| 310167 | enst00000457389 | sg00000198315 | zkscan8-202 | 6 | 28141938 | 28154073 | + | mRNA | protein_coding |
| 310440 | enst00000536028 | sg00000198315 | zkscan8-203 | 6 | 28142211 | 28153079 | + | mRNA | nonsense_mediated_decay |
| -311236 | enst00000648816 | sg00000285703 | al021918.3-201 | 6 | 27491422 | 27519435 | - | lnc_RNA | lncrna |
| -315397 | enst00000603933 | sg00000270666 | al021918.1-201 | 6 | 27515039 | 27515274 | - | pseudogenic_transcript | processed_pseudogene |
| -320170 | enst00000613415 | sg00000278332 | al021918.2-201 | 6 | 27510501 | 27510694 | + | pseudogenic_transcript | processed_pseudogene |
| 329998 | enst00000562227 | sg00000226314 | znf192p1-202 | 6 | 28161769 | 28169588 | + | lnc_RNA | processed_transcript |
| 330010 | enst00000440790 | sg00000226314 | znf192p1-201 | 6 | 28161781 | 28169594 | + | lnc_RNA | processed_transcript |
| 330021 | enst00000570126 | sg00000226314 | znf192p1-205 | 6 | 28161792 | 28163511 | + | lnc_RNA | retained_intron |
| 330647 | enst00000570042 | sg00000226314 | znf192p1-204 | 6 | 28162418 | 28166638 | + | lnc_RNA | retained_intron |
| 334788 | enst00000565888 | sg00000226314 | znf192p1-203 | 6 | 28166559 | 28167368 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 339074 | enst00000625142 | sg00000280107 | al022393.1-201 | 6 | 28170845 | 28172521 | + | unconfirmed_transcript | tec |
| 344417 | enst00000405613 | sg00000216901 | znf603p-201 | 6 | 28176188 | 28176674 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 356279 | enst00000402215 | sg00000218016 | znf192p2-201 | 6 | 28188050 | 28189432 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -357477 | enst00000663193 | sg00000286652 | al021918.5-201 | 6 | 27473194 | 27494436 | + | lnc_RNA | lncrna |
| -357553 | enst00000211936 | sg00000096654 | znf184-201 | 6 | 27450743 | 27473118 | - | mRNA | protein_coding |
| -357990 | enst00000377419 | sg00000096654 | znf184-202 | 6 | 27450820 | 27472681 | - | mRNA | protein_coding |
| -376103 | enst00000648356 | sg00000285849 | al021918.4-201 | 6 | 27454568 | 27457575 | + | lnc_RNA | lncrna |
| 386863 | enst00000469761 | sg00000176933 | tob2p1-201 | 6 | 28217643 | 28218634 | - | pseudogenic_transcript | processed_pseudogene |
| 393115 | enst00000531941 | sg00000137185 | zscan9-206 | 6 | 28224886 | 28227207 | + | mRNA | protein_coding |
| 393493 | enst00000531981 | sg00000137185 | zscan9-208 | 6 | 28225264 | 28227958 | + | mRNA | protein_coding |
| 393504 | enst00000425468 | sg00000137185 | zscan9-202 | 6 | 28225275 | 28233466 | + | mRNA | protein_coding |
| 393521 | enst00000252207 | sg00000137185 | zscan9-201 | 6 | 28225292 | 28233466 | + | mRNA | protein_coding |
| 393521 | enst00000531979 | sg00000137185 | zscan9-207 | 6 | 28225292 | 28233482 | + | mRNA | protein_coding |
| 393528 | enst00000647743 | sg00000137185 | zscan9-209 | 6 | 28225299 | 28233470 | + | mRNA | nonsense_mediated_decay |
| 393568 | enst00000527436 | sg00000137185 | zscan9-204 | 6 | 28225339 | 28229230 | + | mRNA | protein_coding |
| 395150 | enst00000526391 | sg00000137185 | zscan9-203 | 6 | 28226921 | 28232586 | + | mRNA | protein_coding |
| 395241 | enst00000527844 | sg00000137185 | zscan9-205 | 6 | 28227012 | 28233015 | + | mRNA | protein_coding |
| 420498 | enst00000377294 | sg00000187626 | zkscan4-201 | 6 | 28241697 | 28252269 | - | mRNA | protein_coding |
| -422974 | enst00000417812 | sg00000237154 | mcfd2p1-201 | 6 | 27407697 | 27407996 | + | pseudogenic_transcript | processed_pseudogene |
| -423707 | enst00000607727 | sg00000271755 | al031118.1-201 | 6 | 27404010 | 27406964 | - | lnc_RNA | lncrna |
| 427526 | enst00000343684 | sg00000189134 | nkapl-201 | 6 | 28259297 | 28260958 | + | mRNA | protein_coding |
| 435239 | enst00000421553 | sg00000197062 | zscan26-202 | 6 | 28267010 | 28278221 | + | mRNA | protein_coding |
| 435287 | enst00000316606 | sg00000197062 | zscan26-201 | 6 | 28267058 | 28278201 | + | mRNA | protein_coding |
| 435350 | enst00000621053 | sg00000276302 | al021997.3-201 | 6 | 28267121 | 28281580 | + | mRNA | protein_coding |
| 435372 | enst00000617168 | sg00000197062 | zscan26-205 | 6 | 28267143 | 28272703 | + | mRNA | protein_coding |
| 435378 | enst00000611552 | sg00000197062 | zscan26-203 | 6 | 28267149 | 28277159 | + | mRNA | protein_coding |
| 435382 | enst00000623276 | sg00000197062 | zscan26-207 | 6 | 28267153 | 28277530 | + | mRNA | protein_coding |
| 435588 | enst00000614088 | sg00000197062 | zscan26-204 | 6 | 28267359 | 28278221 | + | mRNA | protein_coding |
| 435588 | enst00000619937 | sg00000197062 | zscan26-206 | 6 | 28267359 | 28278224 | + | mRNA | protein_coding |
| -441679 | enst00000461521 | sg00000124613 | znf391-202 | 6 | 27388992 | 27400769 | + | mRNA | protein_coding |
| -441767 | enst00000482767 | sg00000124613 | znf391-204 | 6 | 27388904 | 27391132 | + | lnc_RNA | processed_transcript |
| -441953 | enst00000244576 | sg00000124613 | znf391-201 | 6 | 27388718 | 27403904 | + | mRNA | protein_coding |
| 449801 | enst00000259883 | sg00000137338 | pgbd1-201 | 6 | 28281572 | 28302549 | + | mRNA | protein_coding |
| -456056 | enst00000477999 | sg00000124613 | znf391-203 | 6 | 27374615 | 27399548 | + | lnc_RNA | processed_transcript |
| -470450 | enst00000416749 | sg00000204789 | znf204p-201 | 6 | 27357825 | 27360221 | - | pseudogenic_transcript | processed_pseudogene |
| 484112 | enst00000615674 | sg00000273712 | al021997.2-201 | 6 | 28315613 | 28315883 | - | pseudogenic_transcript | processed_pseudogene |
| 488081 | enst00000605757 | sg00000270326 | al021997.1-201 | 6 | 28319660 | 28319852 | - | pseudogenic_transcript | processed_pseudogene |
| 494946 | enst00000481934 | sg00000235109 | zscan31-218 | 6 | 28324693 | 28326717 | - | lnc_RNA | processed_transcript |
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