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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 |
|---|---|---|---|---|---|---|---|---|
| #125 | 16 | 55330647 | 55332251 | 1604 | 3 | 44 | 1.70024e-16 | 1.35271e-14 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 104 | enst00000573934 | sg00000263207 | ac109462.2-201 | 16 | 55332355 | 55332967 | + | lnc_RNA | lncrna |
| 1337 | enst00000558730 | sg00000259283 | ac109462.1-201 | 16 | 55259969 | 55333588 | - | lnc_RNA | lncrna |
| -4847 | enst00000558315 | sg00000159387 | irx6-202 | 16 | 55325800 | 55327796 | + | lnc_RNA | processed_transcript |
| -6887 | enst00000290552 | sg00000159387 | irx6-201 | 16 | 55323760 | 55330760 | + | mRNA | protein_coding |
| -7961 | enst00000637882 | sg00000283423 | ac109462.3-201 | 16 | 55321575 | 55322686 | - | lnc_RNA | lncrna |
| 20837 | enst00000491087 | sg00000240760 | rpl31p56-201 | 16 | 55352721 | 55353088 | - | pseudogenic_transcript | processed_pseudogene |
| -38972 | enst00000470547 | sg00000239555 | rn7sl841p-201 | 16 | 55291379 | 55291675 | - | ncRNA | misc_rna |
| 57449 | enst00000570308 | sg00000087245 | mmp2-208 | 16 | 55389700 | 55506237 | + | mRNA | protein_coding |
| 93879 | enst00000611626 | sg00000274508 | ac007336.2-201 | 16 | 55425574 | 55426130 | - | lnc_RNA | lncrna |
| 95700 | enst00000620495 | sg00000260135 | mmp2-as1-203 | 16 | 55426797 | 55427951 | - | lnc_RNA | lncrna |
| 96387 | enst00000664911 | sg00000260135 | mmp2-as1-204 | 16 | 55426803 | 55428638 | - | lnc_RNA | lncrna |
| 112508 | enst00000565307 | sg00000260135 | mmp2-as1-201 | 16 | 55429135 | 55444759 | - | lnc_RNA | lncrna |
| 130046 | enst00000569037 | sg00000260135 | mmp2-as1-202 | 16 | 55427558 | 55462297 | - | lnc_RNA | lncrna |
| 146579 | enst00000568715 | sg00000087245 | mmp2-206 | 16 | 55478830 | 55485352 | + | mRNA | protein_coding |
| 146947 | enst00000219070 | sg00000087245 | mmp2-201 | 16 | 55479198 | 55506691 | + | mRNA | protein_coding |
| 147747 | enst00000564864 | sg00000087245 | mmp2-204 | 16 | 55479998 | 55485776 | + | mRNA | protein_coding |
| 148282 | enst00000543485 | sg00000087245 | mmp2-203 | 16 | 55480533 | 55505525 | + | mRNA | protein_coding |
| 149306 | enst00000437642 | sg00000087245 | mmp2-202 | 16 | 55481557 | 55505759 | + | mRNA | protein_coding |
| 154367 | enst00000623886 | sg00000279030 | ac007336.3-201 | 16 | 55486618 | 55488777 | + | unconfirmed_transcript | tec |
| 156411 | enst00000570283 | sg00000087245 | mmp2-207 | 16 | 55488662 | 55502889 | + | mRNA | protein_coding |
| 173124 | enst00000566564 | sg00000087245 | mmp2-205 | 16 | 55505375 | 55506239 | + | mRNA | nonsense_mediated_decay |
| 176821 | enst00000566911 | sg00000087253 | lpcat2-207 | 16 | 55509072 | 55526058 | + | lnc_RNA | retained_intron |
| 176821 | enst00000262134 | sg00000087253 | lpcat2-201 | 16 | 55509072 | 55586666 | + | mRNA | protein_coding |
| 196242 | enst00000564084 | sg00000087253 | lpcat2-204 | 16 | 55528493 | 55542028 | + | mRNA | protein_coding |
| 199788 | enst00000566915 | sg00000087253 | lpcat2-208 | 16 | 55532039 | 55586666 | + | lnc_RNA | retained_intron |
| 205949 | enst00000576365 | sg00000261997 | ac007336.1-201 | 16 | 55538200 | 55542027 | + | lnc_RNA | lncrna |
| 213234 | enst00000563095 | sg00000087253 | lpcat2-203 | 16 | 55545485 | 55574729 | + | lnc_RNA | retained_intron |
| 217055 | enst00000566375 | sg00000087253 | lpcat2-206 | 16 | 55549306 | 55551333 | + | lnc_RNA | retained_intron |
| 224672 | enst00000565056 | sg00000087253 | lpcat2-205 | 16 | 55556923 | 55583012 | + | lnc_RNA | processed_transcript |
| 234433 | enst00000457326 | sg00000256812 | capns2-201 | 16 | 55566684 | 55567687 | + | mRNA | protein_coding |
| 246767 | enst00000562299 | sg00000087253 | lpcat2-202 | 16 | 55579018 | 55583237 | + | lnc_RNA | retained_intron |
| -281329 | enst00000650608 | sg00000285775 | ac109136.1-201 | 16 | 55045700 | 55049318 | - | lnc_RNA | lncrna |
| -322665 | enst00000568888 | sg00000260147 | mtnd5p34-201 | 16 | 55007982 | 55008306 | + | pseudogenic_transcript | processed_pseudogene |
| 323353 | enst00000568943 | sg00000103546 | slc6a2-209 | 16 | 55655604 | 55702346 | + | mRNA | protein_coding |
| 323835 | enst00000568529 | sg00000103546 | slc6a2-207 | 16 | 55656086 | 55694113 | + | mRNA | protein_coding |
| 323859 | enst00000414754 | sg00000103546 | slc6a2-203 | 16 | 55656110 | 55703750 | + | mRNA | protein_coding |
| 324003 | enst00000568655 | sg00000103546 | slc6a2-208 | 16 | 55656254 | 55672131 | + | mRNA | protein_coding |
| 324189 | enst00000379906 | sg00000103546 | slc6a2-202 | 16 | 55656440 | 55703788 | + | mRNA | protein_coding |
| 324367 | enst00000561820 | sg00000103546 | slc6a2-204 | 16 | 55656618 | 55705648 | + | mRNA | protein_coding |
| 324393 | enst00000219833 | sg00000103546 | slc6a2-201 | 16 | 55656644 | 55706192 | + | mRNA | protein_coding |
| 324404 | enst00000566163 | sg00000103546 | slc6a2-205 | 16 | 55656655 | 55702346 | + | mRNA | protein_coding |
| 339420 | enst00000567238 | sg00000103546 | slc6a2-206 | 16 | 55671671 | 55703791 | + | mRNA | protein_coding |
| 368023 | enst00000574918 | sg00000103546 | slc6a2-210 | 16 | 55700274 | 55705853 | + | mRNA | protein_coding |
| 371868 | enst00000624017 | sg00000278928 | ac136621.1-201 | 16 | 55704119 | 55706422 | + | unconfirmed_transcript | tec |
| -391976 | enst00000558156 | sg00000259725 | ac106738.2-202 | 16 | 54938031 | 54938671 | - | lnc_RNA | lncrna |
| -391976 | enst00000559802 | sg00000259725 | ac106738.2-201 | 16 | 54937786 | 54938671 | - | lnc_RNA | lncrna |
| -395734 | enst00000560487 | sg00000259711 | ac106738.1-201 | 16 | 54934913 | 54954665 | + | lnc_RNA | lncrna |
| 395864 | enst00000566467 | sg00000260765 | ces1p2-201 | 16 | 55728115 | 55750111 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -398575 | enst00000558597 | sg00000176842 | irx5-203 | 16 | 54932072 | 54934069 | + | lnc_RNA | retained_intron |
| -399448 | enst00000560154 | sg00000176842 | irx5-204 | 16 | 54931199 | 54933960 | + | mRNA | protein_coding |
| -399448 | enst00000320990 | sg00000176842 | irx5-201 | 16 | 54931199 | 54934485 | + | mRNA | protein_coding |
| -399448 | enst00000620085 | sg00000176842 | irx5-205 | 16 | 54931199 | 54933960 | + | mRNA | protein_coding |
| -399782 | enst00000394636 | sg00000176842 | irx5-202 | 16 | 54930865 | 54934485 | + | mRNA | protein_coding |
| -401458 | enst00000660344 | sg00000245694 | crnde-220 | 16 | 54917956 | 54929189 | - | lnc_RNA | lncrna |
| -401498 | enst00000560208 | sg00000245694 | crnde-209 | 16 | 54924859 | 54929149 | - | lnc_RNA | lncrna |
| -401761 | enst00000558952 | sg00000245694 | crnde-205 | 16 | 54919157 | 54928886 | - | lnc_RNA | lncrna |
| -401789 | enst00000668556 | sg00000245694 | crnde-224 | 16 | 54916492 | 54928858 | - | lnc_RNA | lncrna |
| -401800 | enst00000557792 | sg00000245694 | crnde-203 | 16 | 54918967 | 54928847 | - | lnc_RNA | lncrna |
| -401804 | enst00000661493 | sg00000245694 | crnde-222 | 16 | 54852903 | 54928843 | - | lnc_RNA | lncrna |
| -401809 | enst00000502066 | sg00000245694 | crnde-202 | 16 | 54917968 | 54928838 | - | lnc_RNA | lncrna |
| -401820 | enst00000559598 | sg00000245694 | crnde-207 | 16 | 54917970 | 54928827 | - | lnc_RNA | lncrna |
| -401835 | enst00000560912 | sg00000245694 | crnde-210 | 16 | 54919173 | 54928812 | - | lnc_RNA | lncrna |
| -401931 | enst00000559432 | sg00000245694 | crnde-206 | 16 | 54919066 | 54928716 | - | lnc_RNA | lncrna |
| -402069 | enst00000501177 | sg00000245694 | crnde-201 | 16 | 54918863 | 54928578 | - | lnc_RNA | lncrna |
| -402353 | enst00000655114 | sg00000245694 | crnde-216 | 16 | 54919047 | 54928294 | - | lnc_RNA | lncrna |
| -402457 | enst00000657142 | sg00000245694 | crnde-217 | 16 | 54918942 | 54928190 | - | lnc_RNA | lncrna |
| -402921 | enst00000661312 | sg00000245694 | crnde-221 | 16 | 54918917 | 54927726 | - | lnc_RNA | lncrna |
| -405503 | enst00000613942 | sg00000245694 | crnde-212 | 16 | 54851640 | 54925144 | - | lnc_RNA | lncrna |
| -406759 | enst00000558031 | sg00000245694 | crnde-204 | 16 | 54919011 | 54923888 | - | lnc_RNA | lncrna |
| -410031 | enst00000560029 | sg00000245694 | crnde-208 | 16 | 54918870 | 54920616 | - | lnc_RNA | lncrna |
| 428315 | enst00000574030 | sg00000228695 | ces1p1-204 | 16 | 55760566 | 55773511 | + | lnc_RNA | processed_transcript |
| 428348 | enst00000571348 | sg00000228695 | ces1p1-202 | 16 | 55760599 | 55774926 | + | lnc_RNA | processed_transcript |
| 428350 | enst00000573705 | sg00000228695 | ces1p1-203 | 16 | 55760601 | 55773921 | + | lnc_RNA | processed_transcript |
| 428391 | enst00000421606 | sg00000228695 | ces1p1-201 | 16 | 55760642 | 55793960 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -456477 | enst00000658082 | sg00000245694 | crnde-218 | 16 | 54851643 | 54874170 | - | lnc_RNA | lncrna |
| -456479 | enst00000637011 | sg00000245694 | crnde-214 | 16 | 54847247 | 54874168 | - | lnc_RNA | lncrna |
| 478404 | enst00000563241 | sg00000198848 | ces1-205 | 16 | 55802936 | 55810655 | - | mRNA | protein_coding |
| 480723 | enst00000565568 | sg00000198848 | ces1-207 | 16 | 55802851 | 55812974 | - | mRNA | nonsense_mediated_decay |
| -482328 | enst00000659020 | sg00000245694 | crnde-219 | 16 | 54847247 | 54848319 | - | lnc_RNA | lncrna |
| -482337 | enst00000654070 | sg00000245694 | crnde-215 | 16 | 54847175 | 54848310 | - | lnc_RNA | lncrna |
| -482369 | enst00000635991 | sg00000245694 | crnde-213 | 16 | 54845189 | 54848278 | - | lnc_RNA | lncrna |
| -482398 | enst00000667913 | sg00000245694 | crnde-223 | 16 | 54847247 | 54848249 | - | lnc_RNA | lncrna |
| -482414 | enst00000561591 | sg00000245694 | crnde-211 | 16 | 54847247 | 54848233 | - | lnc_RNA | lncrna |
| -483331 | enst00000659355 | sg00000286357 | ac106742.1-201 | 16 | 54847316 | 54854991 | + | lnc_RNA | lncrna |
| 487329 | enst00000569260 | sg00000198848 | ces1-209 | 16 | 55810571 | 55819580 | - | mRNA | nonsense_mediated_decay |
| 495924 | enst00000566555 | sg00000198848 | ces1-208 | 16 | 55821429 | 55828175 | - | lnc_RNA | processed_transcript |
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