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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 |
|---|---|---|---|---|---|---|---|---|
| #196 | 1 | 90719323 | 90720202 | 879 | 3 | 31 | 2.92112e-14 | 1.48217e-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 |
|---|---|---|---|---|---|---|---|---|---|
| 0 | enst00000660766 | sg00000287076 | ac092805.1-201 | 1 | 90719576 | 90725458 | + | lnc_RNA | lncrna |
| 0 | enst00000659815 | sg00000287076 | ac092805.1-202 | 1 | 90719576 | 90725620 | + | lnc_RNA | lncrna |
| 0 | enst00000662386 | sg00000287076 | ac092805.1-203 | 1 | 90719614 | 90725607 | + | lnc_RNA | lncrna |
| -2021 | enst00000370445 | sg00000143032 | barhl2-201 | 1 | 90711539 | 90717302 | - | mRNA | protein_coding |
| -61573 | enst00000362796 | sg00000199666 | snord3g-201 | 1 | 90657750 | 90657964 | + | snoRNA | snorna |
| 69470 | enst00000664159 | sg00000233593 | linc02609-216 | 1 | 90782984 | 90789672 | - | lnc_RNA | lncrna |
| 111999 | enst00000435649 | sg00000233593 | linc02609-201 | 1 | 90782984 | 90832201 | - | lnc_RNA | lncrna |
| 114487 | enst00000635959 | sg00000233593 | linc02609-207 | 1 | 90831788 | 90834689 | - | lnc_RNA | lncrna |
| 114487 | enst00000636917 | sg00000233593 | linc02609-208 | 1 | 90831874 | 90834689 | - | lnc_RNA | lncrna |
| 114487 | enst00000637260 | sg00000233593 | linc02609-209 | 1 | 90831878 | 90834689 | - | lnc_RNA | lncrna |
| 115360 | enst00000671243 | sg00000233593 | linc02609-225 | 1 | 90831873 | 90835562 | - | lnc_RNA | lncrna |
| 115458 | enst00000662449 | sg00000285532 | linc02788-202 | 1 | 90835660 | 90849460 | + | lnc_RNA | lncrna |
| 115915 | enst00000666920 | sg00000233593 | linc02609-218 | 1 | 90834740 | 90836117 | - | lnc_RNA | lncrna |
| 115959 | enst00000455680 | sg00000233593 | linc02609-203 | 1 | 90829547 | 90836161 | - | lnc_RNA | retained_intron |
| 115972 | enst00000670437 | sg00000233593 | linc02609-223 | 1 | 90830079 | 90836174 | - | lnc_RNA | lncrna |
| 115972 | enst00000652632 | sg00000233593 | linc02609-210 | 1 | 90831953 | 90836174 | - | lnc_RNA | lncrna |
| 116226 | enst00000670363 | sg00000233593 | linc02609-222 | 1 | 90830137 | 90836428 | - | lnc_RNA | lncrna |
| 121385 | enst00000650406 | sg00000285532 | linc02788-201 | 1 | 90841587 | 90849472 | + | lnc_RNA | lncrna |
| 130920 | enst00000655113 | sg00000225446 | linc01763-202 | 1 | 90851122 | 90854607 | + | lnc_RNA | lncrna |
| 131326 | enst00000671059 | sg00000233593 | linc02609-224 | 1 | 90769086 | 90851528 | - | lnc_RNA | lncrna |
| 131416 | enst00000606660 | sg00000233593 | linc02609-204 | 1 | 90829547 | 90851618 | - | lnc_RNA | retained_intron |
| 131418 | enst00000670028 | sg00000233593 | linc02609-221 | 1 | 90837187 | 90851620 | - | lnc_RNA | lncrna |
| 131428 | enst00000657053 | sg00000233593 | linc02609-213 | 1 | 90782513 | 90851630 | - | lnc_RNA | lncrna |
| 131429 | enst00000668679 | sg00000233593 | linc02609-219 | 1 | 90782984 | 90851631 | - | lnc_RNA | lncrna |
| 131439 | enst00000653770 | sg00000233593 | linc02609-211 | 1 | 90807474 | 90851641 | - | lnc_RNA | lncrna |
| 131445 | enst00000634619 | sg00000233593 | linc02609-205 | 1 | 90782984 | 90851647 | - | lnc_RNA | lncrna |
| 131451 | enst00000664774 | sg00000233593 | linc02609-217 | 1 | 90830418 | 90851653 | - | lnc_RNA | lncrna |
| 131451 | enst00000655784 | sg00000233593 | linc02609-212 | 1 | 90830076 | 90851653 | - | lnc_RNA | lncrna |
| 131451 | enst00000669273 | sg00000233593 | linc02609-220 | 1 | 90782513 | 90851653 | - | lnc_RNA | lncrna |
| 131455 | enst00000659034 | sg00000233593 | linc02609-215 | 1 | 90778451 | 90851657 | - | lnc_RNA | lncrna |
| 131456 | enst00000443802 | sg00000233593 | linc02609-202 | 1 | 90829593 | 90851658 | - | lnc_RNA | retained_intron |
| 131456 | enst00000658618 | sg00000233593 | linc02609-214 | 1 | 90828555 | 90851658 | - | lnc_RNA | lncrna |
| 131456 | enst00000635581 | sg00000233593 | linc02609-206 | 1 | 90782984 | 90851658 | - | lnc_RNA | lncrna |
| 131557 | enst00000425185 | sg00000225446 | linc01763-201 | 1 | 90851759 | 90855253 | + | lnc_RNA | lncrna |
| 142718 | enst00000606898 | sg00000272094 | ac091614.1-201 | 1 | 90860550 | 90862920 | - | lnc_RNA | lncrna |
| 173410 | enst00000420457 | sg00000232882 | phka1p1-201 | 1 | 90892992 | 90893612 | - | pseudogenic_transcript | processed_pseudogene |
| -185851 | enst00000435832 | sg00000229201 | linc02787-201 | 1 | 90510910 | 90533472 | - | lnc_RNA | lncrna |
| 198189 | enst00000482709 | sg00000122482 | znf644-209 | 1 | 90916791 | 90918391 | - | lnc_RNA | processed_transcript |
| 215326 | enst00000479798 | sg00000122482 | znf644-207 | 1 | 90916490 | 90935528 | - | lnc_RNA | processed_transcript |
| 219918 | enst00000621077 | sg00000122482 | znf644-212 | 1 | 90937883 | 90940120 | - | mRNA | protein_coding |
| 262168 | enst00000474405 | sg00000122482 | znf644-206 | 1 | 90972744 | 90982370 | - | lnc_RNA | processed_transcript |
| -298927 | enst00000655087 | sg00000287372 | al627316.1-203 | 1 | 90399424 | 90420396 | - | lnc_RNA | lncrna |
| -299176 | enst00000653744 | sg00000287372 | al627316.1-201 | 1 | 90388193 | 90420147 | - | lnc_RNA | lncrna |
| 301255 | enst00000347275 | sg00000122482 | znf644-202 | 1 | 90915304 | 91021457 | - | mRNA | protein_coding |
| 301271 | enst00000370440 | sg00000122482 | znf644-204 | 1 | 90915298 | 91021473 | - | mRNA | protein_coding |
| 301523 | enst00000482467 | sg00000122482 | znf644-208 | 1 | 91020529 | 91021725 | - | lnc_RNA | processed_transcript |
| 301812 | enst00000467231 | sg00000122482 | znf644-205 | 1 | 90916390 | 91022014 | - | lnc_RNA | processed_transcript |
| 301833 | enst00000337393 | sg00000122482 | znf644-201 | 1 | 90915304 | 91022035 | - | mRNA | protein_coding |
| 301853 | enst00000495966 | sg00000122482 | znf644-210 | 1 | 91020448 | 91022055 | - | lnc_RNA | processed_transcript |
| 301879 | enst00000498303 | sg00000122482 | znf644-211 | 1 | 90940949 | 91022081 | - | lnc_RNA | processed_transcript |
| 302070 | enst00000361321 | sg00000122482 | znf644-203 | 1 | 90916185 | 91022272 | - | mRNA | protein_coding |
| 303717 | enst00000425640 | sg00000232393 | rpl5p6-201 | 1 | 91023919 | 91024804 | + | pseudogenic_transcript | processed_pseudogene |
| -318342 | enst00000661553 | sg00000287372 | al627316.1-202 | 1 | 90389826 | 90400981 | - | lnc_RNA | lncrna |
| -465764 | enst00000391157 | sg00000212459 | rnu6-695p-201 | 1 | 90253456 | 90253559 | - | snRNA | snrna |
| -477235 | enst00000663908 | sg00000287406 | ac098656.1-201 | 1 | 90242088 | 90284188 | + | lnc_RNA | lncrna |
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