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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 |
|---|---|---|---|---|---|---|---|---|
| #9 | 17 | 61403712 | 61405954 | 2242 | 3 | 71 | 3.66536e-30 | 4.05022e-27 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 2768 | enst00000586986 | sg00000121068 | tbx2-204 | 17 | 61408722 | 61409466 | + | lnc_RNA | processed_transcript |
| -3347 | enst00000477081 | sg00000121068 | tbx2-203 | 17 | 61400365 | 61409124 | + | lnc_RNA | retained_intron |
| -3469 | enst00000585765 | sg00000267131 | ac005746.2-201 | 17 | 61361668 | 61400243 | - | lnc_RNA | lncrna |
| -3802 | enst00000419047 | sg00000121068 | tbx2-202 | 17 | 61399910 | 61409466 | + | mRNA | nonsense_mediated_decay |
| -3869 | enst00000240328 | sg00000121068 | tbx2-201 | 17 | 61399843 | 61409466 | + | mRNA | protein_coding |
| -4106 | enst00000590421 | sg00000267280 | tbx2-as1-203 | 17 | 61393457 | 61399606 | - | lnc_RNA | lncrna |
| -4124 | enst00000591313 | sg00000267280 | tbx2-as1-204 | 17 | 61393458 | 61399588 | - | lnc_RNA | lncrna |
| -4342 | enst00000589814 | sg00000267280 | tbx2-as1-202 | 17 | 61393458 | 61399370 | - | lnc_RNA | lncrna |
| 5601 | enst00000592009 | sg00000267280 | tbx2-as1-205 | 17 | 61393458 | 61411555 | - | lnc_RNA | lncrna |
| 5797 | enst00000623772 | sg00000187013 | c17orf82-201 | 17 | 61411751 | 61413280 | + | lnc_RNA | lncrna |
| -8265 | enst00000586706 | sg00000267280 | tbx2-as1-201 | 17 | 61393458 | 61395447 | - | lnc_RNA | lncrna |
| -9650 | enst00000592377 | sg00000267280 | tbx2-as1-206 | 17 | 61393456 | 61394062 | - | lnc_RNA | lncrna |
| -15436 | enst00000588720 | sg00000141376 | bcas3-220 | 17 | 61388276 | 61392831 | + | lnc_RNA | retained_intron |
| -20311 | enst00000585495 | sg00000266934 | ac005746.1-202 | 17 | 61383401 | 61384680 | + | lnc_RNA | lncrna |
| -20927 | enst00000589244 | sg00000266934 | ac005746.1-201 | 17 | 61382785 | 61383555 | + | lnc_RNA | lncrna |
| -25882 | enst00000587872 | sg00000141376 | bcas3-214 | 17 | 61377830 | 61380572 | + | lnc_RNA | retained_intron |
| 46450 | enst00000589003 | sg00000121075 | tbx4-203 | 17 | 61452404 | 61478740 | + | mRNA | protein_coding |
| 46468 | enst00000644296 | sg00000121075 | tbx4-208 | 17 | 61452422 | 61485110 | + | mRNA | protein_coding |
| -48557 | enst00000614751 | sg00000273982 | ac005746.3-201 | 17 | 61354763 | 61355155 | - | lnc_RNA | lncrna |
| 50492 | enst00000240335 | sg00000121075 | tbx4-201 | 17 | 61456446 | 61484303 | + | mRNA | protein_coding |
| 50510 | enst00000642491 | sg00000121075 | tbx4-207 | 17 | 61456464 | 61483997 | + | mRNA | protein_coding |
| 57430 | enst00000592766 | sg00000267137 | ac005901.1-201 | 17 | 61460224 | 61463384 | - | lnc_RNA | lncrna |
| 58260 | enst00000593249 | sg00000121075 | tbx4-206 | 17 | 61464214 | 61478789 | + | lnc_RNA | processed_transcript |
| 59839 | enst00000590174 | sg00000121075 | tbx4-205 | 17 | 61465793 | 61480275 | + | lnc_RNA | retained_intron |
| 72397 | enst00000589449 | sg00000121075 | tbx4-204 | 17 | 61478351 | 61483370 | + | lnc_RNA | processed_transcript |
| 72409 | enst00000586874 | sg00000121075 | tbx4-202 | 17 | 61478363 | 61481346 | + | lnc_RNA | processed_transcript |
| -158452 | enst00000588569 | sg00000141376 | bcas3-219 | 17 | 61245260 | 61392273 | + | lnc_RNA | processed_transcript |
| -158496 | enst00000592702 | sg00000141376 | bcas3-229 | 17 | 61245216 | 61392831 | + | lnc_RNA | processed_transcript |
| 185265 | enst00000521764 | sg00000253506 | naca2-201 | 17 | 61590421 | 61591219 | - | mRNA | protein_coding |
| -244350 | enst00000587294 | sg00000141376 | bcas3-213 | 17 | 61159362 | 61392182 | + | lnc_RNA | processed_transcript |
| -246256 | enst00000585812 | sg00000141376 | bcas3-205 | 17 | 61157456 | 61392831 | + | lnc_RNA | processed_transcript |
| -267743 | enst00000666957 | sg00000286997 | ac005856.1-201 | 17 | 61119095 | 61135969 | - | lnc_RNA | lncrna |
| -319207 | enst00000588008 | sg00000141376 | bcas3-215 | 17 | 61084505 | 61087498 | + | lnc_RNA | processed_transcript |
| -325271 | enst00000587002 | sg00000141376 | bcas3-211 | 17 | 61078441 | 61368410 | + | mRNA | protein_coding |
| -333356 | enst00000593107 | sg00000267449 | ac005884.2-201 | 17 | 61069856 | 61070356 | - | lnc_RNA | lncrna |
| -333590 | enst00000588604 | sg00000267207 | ac005884.1-201 | 17 | 61034636 | 61070122 | - | lnc_RNA | lncrna |
| -333841 | enst00000437246 | sg00000227694 | rpl23ap74-201 | 17 | 61069871 | 61070341 | + | pseudogenic_transcript | processed_pseudogene |
| 370526 | enst00000584322 | sg00000136492 | brip1-206 | 17 | 61739057 | 61776480 | - | mRNA | protein_coding |
| 374323 | enst00000583837 | sg00000136492 | brip1-205 | 17 | 61775878 | 61780277 | - | lnc_RNA | processed_transcript |
| -386748 | enst00000592827 | sg00000141376 | bcas3-230 | 17 | 61016964 | 61074988 | + | lnc_RNA | processed_transcript |
| -386750 | enst00000585979 | sg00000141376 | bcas3-206 | 17 | 61016962 | 61368342 | + | lnc_RNA | processed_transcript |
| 387719 | enst00000579028 | sg00000136492 | brip1-204 | 17 | 61776401 | 61793673 | - | mRNA | nonsense_mediated_decay |
| -401155 | enst00000587037 | sg00000141376 | bcas3-212 | 17 | 61002557 | 61037903 | + | lnc_RNA | processed_transcript |
| -416855 | enst00000590352 | sg00000141376 | bcas3-225 | 17 | 60986857 | 61015785 | + | lnc_RNA | processed_transcript |
| 455585 | enst00000577598 | sg00000136492 | brip1-202 | 17 | 61684772 | 61861539 | - | mRNA | protein_coding |
| 457390 | enst00000577913 | sg00000136492 | brip1-203 | 17 | 61857228 | 61863344 | - | mRNA | protein_coding |
| 457574 | enst00000259008 | sg00000136492 | brip1-201 | 17 | 61679139 | 61863528 | - | mRNA | protein_coding |
| 468228 | enst00000365491 | sg00000202361 | ac060798.1-201 | 17 | 61874084 | 61874182 | - | ncRNA | misc_rna |
| 479051 | enst00000583822 | sg00000108506 | ints2-205 | 17 | 61872023 | 61885005 | - | lnc_RNA | retained_intron |
| 479336 | enst00000584967 | sg00000108506 | ints2-206 | 17 | 61877981 | 61885290 | - | lnc_RNA | retained_intron |
| 488232 | enst00000578805 | sg00000108506 | ints2-203 | 17 | 61891577 | 61894186 | - | 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