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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 |
|---|---|---|---|---|---|---|---|---|
| #164 | 13 | 99988942 | 99990064 | 1122 | 3 | 32 | 5.49935e-15 | 3.33482e-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 |
|---|---|---|---|---|---|---|---|---|---|
| -3448 | enst00000481565 | sg00000043355 | zic2-204 | 13 | 99985494 | 99985904 | + | lnc_RNA | processed_transcript |
| -4153 | enst00000477213 | sg00000043355 | zic2-203 | 13 | 99984789 | 99985474 | + | lnc_RNA | processed_transcript |
| -4253 | enst00000468291 | sg00000043355 | zic2-202 | 13 | 99984689 | 99985492 | + | lnc_RNA | processed_transcript |
| -4653 | enst00000490085 | sg00000043355 | zic2-205 | 13 | 99984289 | 99985492 | + | lnc_RNA | processed_transcript |
| -7158 | enst00000376335 | sg00000043355 | zic2-201 | 13 | 99981784 | 99986765 | + | mRNA | protein_coding |
| 7845 | enst00000564841 | sg00000260738 | linc00554-201 | 13 | 99994899 | 99997909 | - | lnc_RNA | lncrna |
| -8908 | enst00000653776 | sg00000288060 | al355338.1-201 | 13 | 99973526 | 99980034 | - | lnc_RNA | lncrna |
| -17033 | enst00000267294 | sg00000139800 | zic5-201 | 13 | 99962964 | 99971909 | - | mRNA | protein_coding |
| -31775 | enst00000670575 | sg00000286757 | al137139.2-201 | 13 | 99841879 | 99957167 | - | lnc_RNA | lncrna |
| -31789 | enst00000671519 | sg00000286757 | al137139.2-207 | 13 | 99864292 | 99957153 | - | lnc_RNA | lncrna |
| -33107 | enst00000656974 | sg00000286757 | al137139.2-205 | 13 | 99852663 | 99955835 | - | lnc_RNA | lncrna |
| -33199 | enst00000659729 | sg00000286757 | al137139.2-204 | 13 | 99852629 | 99955743 | - | lnc_RNA | lncrna |
| -33203 | enst00000661077 | sg00000286757 | al137139.2-203 | 13 | 99844144 | 99955739 | - | lnc_RNA | lncrna |
| 38110 | enst00000455914 | sg00000225999 | ndufa12p1-201 | 13 | 100027769 | 100028174 | - | pseudogenic_transcript | processed_pseudogene |
| 73537 | enst00000451989 | sg00000236554 | asnsp3-201 | 13 | 100062296 | 100063601 | - | pseudogenic_transcript | processed_pseudogene |
| 98784 | enst00000612598 | sg00000274605 | pcca-dt-201 | 13 | 100086031 | 100088848 | - | lnc_RNA | lncrna |
| 98886 | enst00000654763 | sg00000274605 | pcca-dt-202 | 13 | 100053074 | 100088950 | - | lnc_RNA | lncrna |
| 98951 | enst00000376279 | sg00000175198 | pcca-201 | 13 | 100089015 | 100530432 | + | mRNA | protein_coding |
| 98951 | enst00000376286 | sg00000175198 | pcca-203 | 13 | 100089015 | 100530432 | + | mRNA | protein_coding |
| 99029 | enst00000376285 | sg00000175198 | pcca-202 | 13 | 100089093 | 100530435 | + | mRNA | protein_coding |
| 99036 | enst00000647303 | sg00000175198 | pcca-216 | 13 | 100089100 | 100530421 | + | mRNA | nonsense_mediated_decay |
| -109959 | enst00000660452 | sg00000286757 | al137139.2-206 | 13 | 99864134 | 99878983 | - | lnc_RNA | lncrna |
| 112835 | enst00000637358 | sg00000175198 | pcca-214 | 13 | 100102899 | 100237497 | + | mRNA | protein_coding |
| 112835 | enst00000636420 | sg00000175198 | pcca-212 | 13 | 100102899 | 100330672 | + | mRNA | nonsense_mediated_decay |
| 112835 | enst00000636366 | sg00000175198 | pcca-211 | 13 | 100102899 | 100530435 | + | mRNA | protein_coding |
| 112835 | enst00000636475 | sg00000175198 | pcca-213 | 13 | 100102899 | 100530435 | + | mRNA | nonsense_mediated_decay |
| 112835 | enst00000637657 | sg00000175198 | pcca-215 | 13 | 100102899 | 100530437 | + | mRNA | protein_coding |
| -117924 | enst00000425186 | sg00000125246 | clybl-206 | 13 | 99871018 | 99891612 | + | mRNA | protein_coding |
| -122625 | enst00000419700 | sg00000125246 | clybl-205 | 13 | 99866317 | 99892894 | + | mRNA | protein_coding |
| -130081 | enst00000416504 | sg00000125246 | clybl-204 | 13 | 99858861 | 99865238 | + | mRNA | protein_coding |
| -130081 | enst00000443887 | sg00000125246 | clybl-207 | 13 | 99858861 | 99865238 | + | mRNA | protein_coding |
| -133267 | enst00000658325 | sg00000286757 | al137139.2-202 | 13 | 99841921 | 99855675 | - | lnc_RNA | lncrna |
| -147692 | enst00000670400 | sg00000288581 | al137139.3-201 | 13 | 99835813 | 99841250 | - | lnc_RNA | lncrna |
| 159137 | enst00000485946 | sg00000175198 | pcca-209 | 13 | 100149201 | 100161625 | + | lnc_RNA | processed_transcript |
| 161028 | enst00000432924 | sg00000228501 | rpl15p18-201 | 13 | 100150481 | 100151092 | - | pseudogenic_transcript | processed_pseudogene |
| -204959 | enst00000364375 | sg00000201245 | al137139.1-201 | 13 | 99783857 | 99783983 | - | snoRNA | snorna |
| 208405 | enst00000603008 | sg00000270632 | al356575.1-201 | 13 | 100198187 | 100198469 | - | pseudogenic_transcript | processed_pseudogene |
| -259971 | enst00000670609 | sg00000234303 | clybl-as1-202 | 13 | 99726245 | 99728971 | - | lnc_RNA | lncrna |
| -261451 | enst00000416009 | sg00000234303 | clybl-as1-201 | 13 | 99726247 | 99727491 | - | lnc_RNA | lncrna |
| -297971 | enst00000430125 | sg00000227659 | clybl-as2-201 | 13 | 99690081 | 99690971 | - | lnc_RNA | lncrna |
| 303160 | enst00000424527 | sg00000175198 | pcca-205 | 13 | 100293224 | 100425731 | + | mRNA | protein_coding |
| 315712 | enst00000443601 | sg00000175198 | pcca-207 | 13 | 100305776 | 100340259 | + | mRNA | protein_coding |
| -345883 | enst00000583390 | sg00000263615 | mir4306-201 | 13 | 99643059 | 99643149 | + | miRNA | mirna |
| 374895 | enst00000654085 | sg00000287330 | al353697.1-201 | 13 | 100338982 | 100364959 | - | lnc_RNA | lncrna |
| 378408 | enst00000458283 | sg00000175198 | pcca-208 | 13 | 100368472 | 100530432 | + | mRNA | protein_coding |
| 378435 | enst00000413170 | sg00000175198 | pcca-204 | 13 | 100368499 | 100491817 | + | mRNA | protein_coding |
| -382246 | enst00000339105 | sg00000125246 | clybl-201 | 13 | 99606696 | 99892564 | + | mRNA | protein_coding |
| -382252 | enst00000376354 | sg00000125246 | clybl-202 | 13 | 99606690 | 99891613 | + | mRNA | protein_coding |
| -382273 | enst00000376355 | sg00000125246 | clybl-203 | 13 | 99606669 | 99897134 | + | mRNA | protein_coding |
| -398434 | enst00000654441 | sg00000287746 | al139035.2-201 | 13 | 99584014 | 99590508 | - | lnc_RNA | lncrna |
| -406236 | enst00000436148 | sg00000234239 | cfl1p8-201 | 13 | 99582706 | 99583180 | + | pseudogenic_transcript | processed_pseudogene |
| -411830 | enst00000437113 | sg00000234168 | linc01039-201 | 13 | 99577112 | 99580368 | + | lnc_RNA | lncrna |
| -448431 | enst00000466555 | sg00000125304 | tm9sf2-203 | 13 | 99540511 | 99541736 | + | lnc_RNA | processed_transcript |
| -474727 | enst00000463709 | sg00000125304 | tm9sf2-202 | 13 | 99514215 | 99537862 | + | lnc_RNA | processed_transcript |
| -487470 | enst00000376387 | sg00000125304 | tm9sf2-201 | 13 | 99501472 | 99564048 | + | mRNA | protein_coding |
| -487890 | enst00000366259 | sg00000203441 | linc00449-201 | 13 | 99499727 | 99501052 | - | lnc_RNA | lncrna |
| -489636 | enst00000625254 | sg00000280734 | linc01232-201 | 13 | 99496418 | 99499306 | - | lnc_RNA | lncrna |
| -489986 | enst00000642475 | sg00000125304 | tm9sf2-206 | 13 | 99498956 | 99563334 | + | mRNA | protein_coding |
| -490136 | enst00000656995 | sg00000280734 | linc01232-206 | 13 | 99494378 | 99498806 | - | lnc_RNA | lncrna |
| -490193 | enst00000625369 | sg00000280734 | linc01232-203 | 13 | 99495477 | 99498749 | - | lnc_RNA | lncrna |
| -490205 | enst00000626308 | sg00000280710 | al139035.1-201 | 13 | 99498737 | 99501250 | + | lnc_RNA | lncrna |
| 490221 | enst00000451662 | sg00000234650 | pcca-as1-202 | 13 | 100464440 | 100480285 | - | lnc_RNA | lncrna |
| -490418 | enst00000627052 | sg00000125304 | tm9sf2-204 | 13 | 99498524 | 99501315 | + | lnc_RNA | processed_transcript |
| 491093 | enst00000414553 | sg00000234650 | pcca-as1-201 | 13 | 100479559 | 100481157 | - | lnc_RNA | lncrna |
| 491141 | enst00000455958 | sg00000234650 | pcca-as1-203 | 13 | 100479547 | 100481205 | - | lnc_RNA | lncrna |
| -492170 | enst00000630421 | sg00000280734 | linc01232-205 | 13 | 99486962 | 99496772 | - | lnc_RNA | lncrna |
| -492204 | enst00000626729 | sg00000280734 | linc01232-204 | 13 | 99491475 | 99496738 | - | lnc_RNA | lncrna |
| -494799 | enst00000625287 | sg00000280734 | linc01232-202 | 13 | 99491468 | 99494143 | - | lnc_RNA | retained_intron |
| 499904 | enst00000621936 | sg00000175198 | pcca-210 | 13 | 100489968 | 100491817 | + | lnc_RNA | retained_intron |
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