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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 |
|---|---|---|---|---|---|---|---|---|
| #19 | 6 | 108174295 | 108176232 | 1937 | 3 | 62 | 7.48685e-27 | 3.91878e-24 |
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 | enst00000484978 | sg00000112333 | nr2e1-204 | 6 | 108176104 | 108178147 | + | lnc_RNA | processed_transcript |
| 2639 | enst00000624856 | sg00000279398 | al078596.1-201 | 6 | 108178871 | 108179317 | + | unconfirmed_transcript | tec |
| -5532 | enst00000426403 | sg00000112333 | nr2e1-203 | 6 | 108168763 | 108176626 | + | mRNA | protein_coding |
| -6272 | enst00000368983 | sg00000112333 | nr2e1-201 | 6 | 108168023 | 108188802 | + | mRNA | protein_coding |
| -8237 | enst00000368986 | sg00000112333 | nr2e1-202 | 6 | 108166058 | 108188809 | + | mRNA | protein_coding |
| -8441 | enst00000492070 | sg00000081087 | ostm1-206 | 6 | 108122336 | 108165854 | - | lnc_RNA | processed_transcript |
| -8455 | enst00000440575 | sg00000081087 | ostm1-202 | 6 | 108044831 | 108165840 | - | mRNA | protein_coding |
| -50662 | enst00000441184 | sg00000225174 | ostm1-as1-202 | 6 | 108123633 | 108159392 | + | lnc_RNA | lncrna |
| -50780 | enst00000426008 | sg00000225174 | ostm1-as1-201 | 6 | 108123515 | 108156698 | + | lnc_RNA | lncrna |
| -50838 | enst00000658282 | sg00000225174 | ostm1-as1-203 | 6 | 108123457 | 108157875 | + | lnc_RNA | lncrna |
| 75982 | enst00000431564 | sg00000233511 | z98742.2-201 | 6 | 108252214 | 108252400 | + | pseudogenic_transcript | processed_pseudogene |
| 76169 | enst00000391223 | sg00000212525 | rna5sp212-201 | 6 | 108252401 | 108252507 | + | pseudogenic_transcript | rrna_pseudogene |
| 84732 | enst00000426155 | sg00000112335 | snx3-204 | 6 | 108211513 | 108260964 | - | mRNA | protein_coding |
| 84808 | enst00000230085 | sg00000112335 | snx3-201 | 6 | 108211222 | 108261040 | - | mRNA | protein_coding |
| 85012 | enst00000349379 | sg00000112335 | snx3-202 | 6 | 108212005 | 108261244 | - | mRNA | protein_coding |
| 85014 | enst00000368979 | sg00000112335 | snx3-203 | 6 | 108211513 | 108261246 | - | mRNA | nonsense_mediated_decay |
| 85056 | enst00000667578 | sg00000286562 | z98742.4-201 | 6 | 108261288 | 108269200 | + | lnc_RNA | lncrna |
| 99410 | enst00000419801 | sg00000230248 | z98742.1-201 | 6 | 108275642 | 108276546 | + | lnc_RNA | lncrna |
| -99554 | enst00000467960 | sg00000081087 | ostm1-203 | 6 | 108064185 | 108074741 | - | lnc_RNA | processed_transcript |
| -99554 | enst00000193322 | sg00000081087 | ostm1-201 | 6 | 108041409 | 108074741 | - | mRNA | protein_coding |
| -113477 | enst00000364811 | sg00000238490 | z98200.1-201 | 6 | 108060818 | 108060930 | + | ncRNA | misc_rna |
| 116534 | enst00000384247 | sg00000206974 | rnu6-1144p-201 | 6 | 108292766 | 108292869 | + | snRNA | snrna |
| 118759 | enst00000430458 | sg00000135537 | afg1l-203 | 6 | 108294991 | 108346990 | + | lnc_RNA | processed_transcript |
| 118822 | enst00000368977 | sg00000135537 | afg1l-201 | 6 | 108295054 | 108526001 | + | mRNA | protein_coding |
| 118969 | enst00000421954 | sg00000135537 | afg1l-202 | 6 | 108295201 | 108523117 | + | mRNA | protein_coding |
| 119521 | enst00000437715 | sg00000135537 | afg1l-205 | 6 | 108295753 | 108356751 | + | mRNA | protein_coding |
| -123229 | enst00000472669 | sg00000081087 | ostm1-204 | 6 | 108044379 | 108051066 | - | lnc_RNA | processed_transcript |
| -124627 | enst00000477774 | sg00000081087 | ostm1-205 | 6 | 108044733 | 108049668 | - | lnc_RNA | processed_transcript |
| -130057 | enst00000492130 | sg00000081087 | ostm1-207 | 6 | 108041472 | 108044238 | - | lnc_RNA | processed_transcript |
| 141847 | enst00000418637 | sg00000238055 | z98742.3-201 | 6 | 108318079 | 108318404 | + | pseudogenic_transcript | processed_pseudogene |
| -143577 | enst00000607298 | sg00000271734 | z98200.2-201 | 6 | 108030249 | 108030718 | - | lnc_RNA | lncrna |
| -168727 | enst00000417878 | sg00000225093 | rpl3p7-201 | 6 | 108004357 | 108005568 | - | pseudogenic_transcript | processed_pseudogene |
| 180458 | enst00000431865 | sg00000135537 | afg1l-204 | 6 | 108356690 | 108522334 | + | mRNA | nonsense_mediated_decay |
| 183631 | enst00000624715 | sg00000279498 | al356121.2-201 | 6 | 108359084 | 108359863 | - | unconfirmed_transcript | tec |
| -188264 | enst00000423135 | sg00000231112 | mthfd2p3-201 | 6 | 107985811 | 107986031 | - | pseudogenic_transcript | processed_pseudogene |
| -188522 | enst00000517281 | sg00000253090 | al024507.2-201 | 6 | 107985659 | 107985773 | - | snoRNA | snorna |
| -188605 | enst00000412741 | sg00000224987 | al024507.1-201 | 6 | 107985089 | 107985690 | - | pseudogenic_transcript | processed_pseudogene |
| 196695 | enst00000442911 | sg00000238079 | al356121.1-201 | 6 | 108372772 | 108372927 | - | pseudogenic_transcript | processed_pseudogene |
| 211280 | enst00000436728 | sg00000227072 | al353706.1-201 | 6 | 108387512 | 108388080 | + | pseudogenic_transcript | processed_pseudogene |
| 215841 | enst00000363929 | sg00000200799 | rnu6-770p-201 | 6 | 108392073 | 108392177 | + | snRNA | snrna |
| -216087 | enst00000369002 | sg00000025796 | sec63-201 | 6 | 107867756 | 107958208 | - | mRNA | protein_coding |
| -216184 | enst00000446496 | sg00000025796 | sec63-203 | 6 | 107924818 | 107958111 | - | mRNA | nonsense_mediated_decay |
| -216253 | enst00000460009 | sg00000025796 | sec63-205 | 6 | 107954584 | 107958042 | - | lnc_RNA | processed_transcript |
| -216364 | enst00000484803 | sg00000025796 | sec63-209 | 6 | 107911168 | 107957931 | - | lnc_RNA | retained_intron |
| -216882 | enst00000606070 | sg00000272476 | al024507.3-201 | 6 | 107957413 | 107959986 | + | lnc_RNA | lncrna |
| -216955 | enst00000429168 | sg00000025796 | sec63-202 | 6 | 107909008 | 107957340 | - | mRNA | protein_coding |
| -242495 | enst00000434149 | sg00000232778 | rpl23ap50-201 | 6 | 107931800 | 107932254 | + | pseudogenic_transcript | processed_pseudogene |
| -244207 | enst00000459408 | sg00000238420 | rnu6-437p-201 | 6 | 107930088 | 107930182 | + | snRNA | snrna |
| -265136 | enst00000489455 | sg00000025796 | sec63-210 | 6 | 107906465 | 107909159 | - | lnc_RNA | retained_intron |
| -271395 | enst00000466419 | sg00000025796 | sec63-207 | 6 | 107893580 | 107902900 | - | lnc_RNA | retained_intron |
| -290828 | enst00000473746 | sg00000025796 | sec63-208 | 6 | 107872885 | 107883467 | - | lnc_RNA | retained_intron |
| -291183 | enst00000465210 | sg00000025796 | sec63-206 | 6 | 107880960 | 107883112 | - | lnc_RNA | retained_intron |
| -296895 | enst00000459782 | sg00000025796 | sec63-204 | 6 | 107870765 | 107877400 | - | lnc_RNA | retained_intron |
| 300747 | enst00000486863 | sg00000135537 | afg1l-207 | 6 | 108476979 | 108522465 | + | lnc_RNA | retained_intron |
| 346905 | enst00000481842 | sg00000135537 | afg1l-206 | 6 | 108523137 | 108526796 | + | lnc_RNA | processed_transcript |
| -349978 | enst00000369022 | sg00000146285 | scml4-203 | 6 | 107704104 | 107824317 | - | mRNA | protein_coding |
| -349982 | enst00000369020 | sg00000146285 | scml4-201 | 6 | 107702154 | 107824313 | - | mRNA | protein_coding |
| -349983 | enst00000473515 | sg00000146285 | scml4-209 | 6 | 107718955 | 107824312 | - | lnc_RNA | retained_intron |
| -350001 | enst00000463507 | sg00000146285 | scml4-208 | 6 | 107720671 | 107824294 | - | lnc_RNA | retained_intron |
| -350009 | enst00000426221 | sg00000146285 | scml4-205 | 6 | 107740065 | 107824286 | - | mRNA | nonsense_mediated_decay |
| 374975 | enst00000603860 | sg00000271608 | al391646.1-201 | 6 | 108551018 | 108551207 | - | pseudogenic_transcript | processed_pseudogene |
| 382054 | enst00000659932 | sg00000287044 | al139106.1-201 | 6 | 108441880 | 108558286 | - | lnc_RNA | lncrna |
| 383603 | enst00000343882 | sg00000118689 | foxo3-201 | 6 | 108559835 | 108684774 | + | mRNA | protein_coding |
| 384685 | enst00000406360 | sg00000118689 | foxo3-202 | 6 | 108560917 | 108684774 | + | mRNA | protein_coding |
| -402044 | enst00000369021 | sg00000146285 | scml4-202 | 6 | 107718954 | 107772251 | - | mRNA | protein_coding |
| -402044 | enst00000459992 | sg00000146285 | scml4-207 | 6 | 107719730 | 107772251 | - | lnc_RNA | retained_intron |
| -402044 | enst00000440927 | sg00000146285 | scml4-206 | 6 | 107744949 | 107772251 | - | mRNA | protein_coding |
| -430241 | enst00000479803 | sg00000146285 | scml4-211 | 6 | 107720709 | 107744054 | - | lnc_RNA | processed_transcript |
| -441900 | enst00000369025 | sg00000146285 | scml4-204 | 6 | 107704651 | 107732395 | - | mRNA | protein_coding |
| 442053 | enst00000434672 | sg00000228976 | sumo2p8-201 | 6 | 108618000 | 108618285 | - | pseudogenic_transcript | processed_pseudogene |
| -442192 | enst00000476798 | sg00000146285 | scml4-210 | 6 | 107718445 | 107732103 | - | lnc_RNA | retained_intron |
| -474077 | enst00000623300 | sg00000280135 | al096816.1-201 | 6 | 107697299 | 107700218 | - | unconfirmed_transcript | tec |
| 480114 | enst00000540898 | sg00000118689 | foxo3-203 | 6 | 108656346 | 108680751 | + | 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