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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 |
|---|---|---|---|---|---|---|---|---|
| #175 | 1 | 229407010 | 229408217 | 1207 | 3 | 35 | 1.34225e-14 | 7.62784e-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 |
|---|---|---|---|---|---|---|---|---|---|
| 2550 | enst00000516242 | sg00000252051 | rn7skp276-201 | 1 | 229410500 | 229410767 | - | ncRNA | misc_rna |
| 16803 | enst00000432935 | sg00000230331 | al160004.2-201 | 1 | 229425020 | 229425650 | + | pseudogenic_transcript | processed_pseudogene |
| -23882 | enst00000516697 | sg00000252506 | rnu6-180p-201 | 1 | 229383128 | 229383188 | + | snRNA | snrna |
| 25877 | enst00000366684 | sg00000143632 | acta1-202 | 1 | 229431245 | 229434094 | - | mRNA | protein_coding |
| 25881 | enst00000366683 | sg00000143632 | acta1-201 | 1 | 229431249 | 229434098 | - | mRNA | protein_coding |
| 32803 | enst00000434311 | sg00000226920 | al160004.1-201 | 1 | 229440284 | 229441020 | - | lnc_RNA | lncrna |
| 42534 | enst00000490352 | sg00000069248 | nup133-204 | 1 | 229441779 | 229450751 | - | lnc_RNA | processed_transcript |
| 42853 | enst00000485119 | sg00000069248 | nup133-203 | 1 | 229448772 | 229451070 | - | lnc_RNA | processed_transcript |
| -63716 | enst00000483092 | sg00000154429 | ccsap-204 | 1 | 229323539 | 229343294 | - | lnc_RNA | processed_transcript |
| -63963 | enst00000284617 | sg00000154429 | ccsap-201 | 1 | 229321015 | 229343047 | - | mRNA | protein_coding |
| -64493 | enst00000366687 | sg00000154429 | ccsap-203 | 1 | 229321011 | 229342517 | - | mRNA | protein_coding |
| -66377 | enst00000366686 | sg00000154429 | ccsap-202 | 1 | 229321515 | 229340633 | - | mRNA | protein_coding |
| -87607 | enst00000418348 | sg00000237481 | al117350.2-201 | 1 | 229319403 | 229323087 | + | lnc_RNA | lncrna |
| 100109 | enst00000366678 | sg00000069248 | nup133-202 | 1 | 229499167 | 229508326 | - | lnc_RNA | processed_transcript |
| 100124 | enst00000261396 | sg00000069248 | nup133-201 | 1 | 229440259 | 229508341 | - | mRNA | protein_coding |
| 100152 | enst00000417605 | sg00000223635 | al121990.1-201 | 1 | 229508369 | 229514272 | + | lnc_RNA | lncrna |
| -101875 | enst00000366688 | sg00000213029 | al117350.1-201 | 1 | 229305135 | 229305326 | + | mRNA | protein_coding |
| 110886 | enst00000498158 | sg00000135776 | abcb10-203 | 1 | 229517797 | 229519103 | - | lnc_RNA | processed_transcript |
| -120525 | enst00000489342 | sg00000168118 | rab4a-204 | 1 | 229286485 | 229289199 | + | lnc_RNA | processed_transcript |
| 123685 | enst00000486755 | sg00000135776 | abcb10-202 | 1 | 229526062 | 229531902 | - | lnc_RNA | processed_transcript |
| 126972 | enst00000362802 | sg00000199672 | rnu4-21p-201 | 1 | 229535064 | 229535189 | - | snRNA | snrna |
| -135768 | enst00000660017 | sg00000177788 | al162595.1-205 | 1 | 229263943 | 229271242 | - | lnc_RNA | lncrna |
| -135816 | enst00000473894 | sg00000168118 | rab4a-202 | 1 | 229271194 | 229303894 | + | lnc_RNA | processed_transcript |
| -135865 | enst00000654028 | sg00000177788 | al162595.1-201 | 1 | 229256892 | 229271145 | - | lnc_RNA | lncrna |
| -135899 | enst00000366690 | sg00000168118 | rab4a-201 | 1 | 229271111 | 229305894 | + | mRNA | protein_coding |
| -135935 | enst00000481981 | sg00000168118 | rab4a-203 | 1 | 229271075 | 229288882 | + | lnc_RNA | retained_intron |
| -135943 | enst00000436334 | sg00000177788 | al162595.1-207 | 1 | 229267265 | 229271067 | - | lnc_RNA | lncrna |
| -135948 | enst00000618010 | sg00000168118 | rab4a-205 | 1 | 229271062 | 229305891 | + | mRNA | protein_coding |
| -135959 | enst00000662321 | sg00000177788 | al162595.1-206 | 1 | 229267157 | 229271051 | - | lnc_RNA | lncrna |
| -135970 | enst00000653511 | sg00000177788 | al162595.1-202 | 1 | 229256933 | 229271040 | - | lnc_RNA | lncrna |
| -135974 | enst00000656366 | sg00000177788 | al162595.1-203 | 1 | 229257121 | 229271036 | - | lnc_RNA | lncrna |
| -136007 | enst00000429227 | sg00000177788 | al162595.1-204 | 1 | 229258281 | 229271003 | - | lnc_RNA | lncrna |
| 141688 | enst00000364622 | sg00000201492 | rna5sp78-201 | 1 | 229549905 | 229550022 | + | pseudogenic_transcript | rrna_pseudogene |
| 150490 | enst00000344517 | sg00000135776 | abcb10-201 | 1 | 229516582 | 229558707 | - | mRNA | protein_coding |
| -157374 | enst00000323223 | sg00000177800 | tmem78-201 | 1 | 229249636 | 229251810 | + | lnc_RNA | lncrna |
| 162315 | enst00000425149 | sg00000229367 | hmgn2p19-201 | 1 | 229570532 | 229570796 | + | pseudogenic_transcript | processed_pseudogene |
| -164108 | enst00000651412 | sg00000233920 | al162595.2-201 | 1 | 229223457 | 229242902 | - | lnc_RNA | lncrna |
| -179448 | enst00000430677 | sg00000233920 | al162595.2-202 | 1 | 229223461 | 229227562 | - | lnc_RNA | lncrna |
| -201582 | enst00000666388 | sg00000236975 | linc02814-204 | 1 | 229092819 | 229205428 | - | lnc_RNA | lncrna |
| 206265 | enst00000366676 | sg00000135801 | taf5l-204 | 1 | 229593111 | 229614482 | - | mRNA | protein_coding |
| 217753 | enst00000366675 | sg00000135801 | taf5l-203 | 1 | 229599194 | 229625970 | - | mRNA | protein_coding |
| 217821 | enst00000477957 | sg00000135801 | taf5l-205 | 1 | 229606834 | 229626038 | - | lnc_RNA | processed_transcript |
| 217830 | enst00000366674 | sg00000135801 | taf5l-202 | 1 | 229614157 | 229626047 | - | mRNA | protein_coding |
| 217830 | enst00000258281 | sg00000135801 | taf5l-201 | 1 | 229593121 | 229626047 | - | mRNA | protein_coding |
| 218030 | enst00000258243 | sg00000135763 | urb2-201 | 1 | 229626247 | 229660200 | + | mRNA | protein_coding |
| -222915 | enst00000662083 | sg00000236975 | linc02814-203 | 1 | 229087114 | 229184095 | - | lnc_RNA | lncrna |
| 242630 | enst00000434387 | sg00000135763 | urb2-202 | 1 | 229650847 | 229659126 | + | mRNA | protein_coding |
| 281687 | enst00000434580 | sg00000213028 | al354983.1-201 | 1 | 229688999 | 229689904 | - | pseudogenic_transcript | processed_pseudogene |
| 297644 | enst00000452520 | sg00000225984 | hmgb1p26-201 | 1 | 229705234 | 229705861 | - | pseudogenic_transcript | processed_pseudogene |
| -312105 | enst00000433734 | sg00000236975 | linc02814-201 | 1 | 229092815 | 229094905 | - | lnc_RNA | lncrna |
| -312115 | enst00000658958 | sg00000236975 | linc02814-202 | 1 | 229089200 | 229094895 | - | lnc_RNA | lncrna |
| -364839 | enst00000438679 | sg00000229840 | isca1p2-201 | 1 | 229042171 | 229042591 | + | pseudogenic_transcript | processed_pseudogene |
| -368736 | enst00000632635 | sg00000282111 | linc02815-201 | 1 | 229022773 | 229038274 | - | lnc_RNA | lncrna |
| 483785 | enst00000669450 | sg00000227043 | linc01682-204 | 1 | 229871965 | 229892002 | - | lnc_RNA | lncrna |
| 483791 | enst00000650825 | sg00000227043 | linc01682-202 | 1 | 229812917 | 229892008 | - | lnc_RNA | lncrna |
| 483804 | enst00000661713 | sg00000227043 | linc01682-203 | 1 | 229869435 | 229892021 | - | lnc_RNA | lncrna |
| 483815 | enst00000435973 | sg00000227043 | linc01682-201 | 1 | 229875546 | 229892032 | - | lnc_RNA | lncrna |
| 483829 | enst00000669533 | sg00000227043 | linc01682-205 | 1 | 229875555 | 229892046 | - | 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