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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 |
|---|---|---|---|---|---|---|---|---|
| #149 | 6 | 10417025 | 10418033 | 1008 | 3 | 35 | 1.22457e-15 | 8.17336e-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 |
|---|---|---|---|---|---|---|---|---|---|
| 0 | enst00000490875 | sg00000137203 | tfap2a-217 | 6 | 10404621 | 10417207 | - | lnc_RNA | processed_transcript |
| -835 | enst00000482890 | sg00000137203 | tfap2a-213 | 6 | 10398013 | 10416190 | - | mRNA | protein_coding |
| 1521 | enst00000464323 | sg00000137203 | tfap2a-206 | 6 | 10409086 | 10419554 | - | lnc_RNA | retained_intron |
| 1590 | enst00000486038 | sg00000137203 | tfap2a-214 | 6 | 10418189 | 10419623 | - | lnc_RNA | processed_transcript |
| 1605 | enst00000319516 | sg00000137203 | tfap2a-201 | 6 | 10397872 | 10419638 | - | mRNA | protein_coding |
| 1626 | enst00000473652 | sg00000137203 | tfap2a-209 | 6 | 10404668 | 10419659 | - | lnc_RNA | processed_transcript |
| -1819 | enst00000488193 | sg00000137203 | tfap2a-215 | 6 | 10397915 | 10415206 | - | mRNA | nonsense_mediated_decay |
| -1951 | enst00000379613 | sg00000137203 | tfap2a-203 | 6 | 10396677 | 10415074 | - | mRNA | protein_coding |
| -2025 | enst00000498450 | sg00000137203 | tfap2a-219 | 6 | 10402538 | 10415000 | - | mRNA | protein_coding |
| -2040 | enst00000478375 | sg00000137203 | tfap2a-212 | 6 | 10402026 | 10414985 | - | lnc_RNA | retained_intron |
| -2040 | enst00000673625 | sg00000137203 | tfap2a-220 | 6 | 10398417 | 10414985 | - | mRNA | protein_coding |
| -2040 | enst00000466073 | sg00000137203 | tfap2a-208 | 6 | 10398602 | 10414985 | - | mRNA | protein_coding |
| -2447 | enst00000443546 | sg00000229950 | tfap2a-as1-202 | 6 | 10414578 | 10415722 | + | lnc_RNA | lncrna |
| -4146 | enst00000465858 | sg00000137203 | tfap2a-207 | 6 | 10409997 | 10412879 | - | mRNA | protein_coding |
| -4636 | enst00000379608 | sg00000137203 | tfap2a-202 | 6 | 10396677 | 10412389 | - | mRNA | protein_coding |
| -4850 | enst00000489805 | sg00000137203 | tfap2a-216 | 6 | 10397410 | 10412175 | - | mRNA | nonsense_mediated_decay |
| -4979 | enst00000474952 | sg00000137203 | tfap2a-210 | 6 | 10406136 | 10412046 | - | lnc_RNA | retained_intron |
| -6007 | enst00000497266 | sg00000137203 | tfap2a-218 | 6 | 10398688 | 10411018 | - | lnc_RNA | processed_transcript |
| -6083 | enst00000462727 | sg00000137203 | tfap2a-205 | 6 | 10406794 | 10410942 | - | lnc_RNA | processed_transcript |
| -6931 | enst00000475264 | sg00000137203 | tfap2a-211 | 6 | 10400714 | 10410094 | - | mRNA | protein_coding |
| -7685 | enst00000420777 | sg00000229950 | tfap2a-as1-201 | 6 | 10409340 | 10416446 | + | lnc_RNA | lncrna |
| 8143 | enst00000420389 | sg00000228478 | al138885.2-201 | 6 | 10423140 | 10426176 | - | lnc_RNA | lncrna |
| 8590 | enst00000647739 | sg00000285759 | al138885.4-201 | 6 | 10426623 | 10429110 | + | lnc_RNA | lncrna |
| -12431 | enst00000461628 | sg00000137203 | tfap2a-204 | 6 | 10393186 | 10404594 | - | mRNA | protein_coding |
| -12523 | enst00000645232 | sg00000285278 | al138885.3-201 | 6 | 10404502 | 10407928 | + | lnc_RNA | lncrna |
| 16283 | enst00000449333 | sg00000229401 | mir5689hg-202 | 6 | 10434316 | 10452247 | + | lnc_RNA | lncrna |
| 16296 | enst00000366312 | sg00000229401 | mir5689hg-201 | 6 | 10434329 | 10456781 | + | lnc_RNA | lncrna |
| 16444 | enst00000656574 | sg00000183674 | linc00518-207 | 6 | 10429257 | 10434477 | - | lnc_RNA | lncrna |
| 16462 | enst00000472178 | sg00000183674 | linc00518-201 | 6 | 10429709 | 10434495 | - | lnc_RNA | lncrna |
| 16784 | enst00000491317 | sg00000183674 | linc00518-204 | 6 | 10429796 | 10434817 | - | lnc_RNA | lncrna |
| 16802 | enst00000479822 | sg00000183674 | linc00518-202 | 6 | 10429262 | 10434835 | - | lnc_RNA | lncrna |
| 16841 | enst00000487130 | sg00000183674 | linc00518-203 | 6 | 10429548 | 10434874 | - | lnc_RNA | lncrna |
| 16924 | enst00000662081 | sg00000183674 | linc00518-208 | 6 | 10429263 | 10434957 | - | lnc_RNA | lncrna |
| 16970 | enst00000496285 | sg00000183674 | linc00518-205 | 6 | 10429255 | 10435003 | - | lnc_RNA | lncrna |
| 16982 | enst00000655125 | sg00000183674 | linc00518-206 | 6 | 10429255 | 10435015 | - | lnc_RNA | lncrna |
| 21684 | enst00000581998 | sg00000263705 | mir5689-201 | 6 | 10439717 | 10439794 | + | miRNA | mirna |
| 42508 | enst00000445390 | sg00000238076 | mrpl48p1-201 | 6 | 10459906 | 10460541 | - | pseudogenic_transcript | processed_pseudogene |
| -50443 | enst00000405921 | sg00000216781 | al138885.1-201 | 6 | 10365593 | 10366582 | - | pseudogenic_transcript | processed_pseudogene |
| 60469 | enst00000431401 | sg00000231056 | linc02522-201 | 6 | 10474500 | 10478502 | - | lnc_RNA | lncrna |
| 74190 | enst00000410107 | sg00000111846 | gcnt2-205 | 6 | 10492223 | 10627222 | + | mRNA | protein_coding |
| 74191 | enst00000489225 | sg00000111846 | gcnt2-214 | 6 | 10492224 | 10626972 | + | lnc_RNA | processed_transcript |
| 74193 | enst00000488742 | sg00000111846 | gcnt2-213 | 6 | 10492226 | 10528707 | + | lnc_RNA | processed_transcript |
| 96249 | enst00000401900 | sg00000216359 | al139039.1-201 | 6 | 10514282 | 10514973 | + | pseudogenic_transcript | processed_pseudogene |
| 96513 | enst00000413129 | sg00000237685 | al139039.3-201 | 6 | 10511036 | 10514546 | - | lnc_RNA | lncrna |
| 103250 | enst00000495262 | sg00000111846 | gcnt2-216 | 6 | 10521283 | 10629368 | + | mRNA | protein_coding |
| 103276 | enst00000474983 | sg00000111846 | gcnt2-209 | 6 | 10521309 | 10530267 | + | lnc_RNA | retained_intron |
| 103299 | enst00000397423 | sg00000111846 | gcnt2-204 | 6 | 10521332 | 10626947 | + | lnc_RNA | processed_transcript |
| 103318 | enst00000475577 | sg00000111846 | gcnt2-210 | 6 | 10521351 | 10626616 | + | lnc_RNA | processed_transcript |
| 103387 | enst00000489819 | sg00000111846 | gcnt2-215 | 6 | 10521420 | 10626557 | + | lnc_RNA | processed_transcript |
| 103452 | enst00000474518 | sg00000111846 | gcnt2-208 | 6 | 10521485 | 10621422 | + | lnc_RNA | processed_transcript |
| 109333 | enst00000483204 | sg00000111846 | gcnt2-211 | 6 | 10527366 | 10529279 | + | lnc_RNA | retained_intron |
| 110323 | enst00000379597 | sg00000111846 | gcnt2-203 | 6 | 10528356 | 10629367 | + | mRNA | protein_coding |
| 111764 | enst00000485764 | sg00000111846 | gcnt2-212 | 6 | 10529797 | 10626464 | + | lnc_RNA | processed_transcript |
| 111779 | enst00000461400 | sg00000111846 | gcnt2-207 | 6 | 10529812 | 10621645 | + | lnc_RNA | retained_intron |
| 137974 | enst00000316170 | sg00000111846 | gcnt2-202 | 6 | 10556007 | 10629367 | + | mRNA | protein_coding |
| 138391 | enst00000640968 | sg00000111846 | gcnt2-217 | 6 | 10556424 | 10557993 | + | mRNA | protein_coding |
| 138768 | enst00000459872 | sg00000111846 | gcnt2-206 | 6 | 10556801 | 10619441 | + | lnc_RNA | processed_transcript |
| 157194 | enst00000407436 | sg00000217181 | al139039.2-201 | 6 | 10574749 | 10575227 | - | pseudogenic_transcript | processed_pseudogene |
| 167713 | enst00000265012 | sg00000111846 | gcnt2-201 | 6 | 10585746 | 10629368 | + | mRNA | protein_coding |
| -194989 | enst00000408656 | sg00000221583 | rnu6atac21p-201 | 6 | 10222036 | 10222161 | + | snRNA | snrna |
| -202663 | enst00000417077 | sg00000229765 | al354868.1-201 | 6 | 10213881 | 10214362 | - | pseudogenic_transcript | processed_pseudogene |
| -205417 | enst00000481704 | sg00000181355 | ofcc1-209 | 6 | 9939289 | 10211608 | - | lnc_RNA | processed_transcript |
| -205485 | enst00000462111 | sg00000181355 | ofcc1-203 | 6 | 10060702 | 10211540 | - | lnc_RNA | processed_transcript |
| 215729 | enst00000379591 | sg00000205318 | gcnt2p1-201 | 6 | 10633762 | 10634695 | + | pseudogenic_transcript | processed_pseudogene |
| 241465 | enst00000649568 | sg00000285763 | al358777.3-201 | 6 | 10659498 | 10692860 | + | lnc_RNA | lncrna |
| 256735 | enst00000364178 | sg00000201048 | al358777.1-201 | 6 | 10674658 | 10674768 | - | ncRNA | misc_rna |
| 269517 | enst00000426700 | sg00000137434 | c6orf52-203 | 6 | 10671422 | 10687550 | - | mRNA | protein_coding |
| 276500 | enst00000460742 | sg00000137434 | c6orf52-204 | 6 | 10671418 | 10694533 | - | mRNA | protein_coding |
| 276500 | enst00000467832 | sg00000137434 | c6orf52-205 | 6 | 10671422 | 10694533 | - | lnc_RNA | processed_transcript |
| 276573 | enst00000259983 | sg00000137434 | c6orf52-201 | 6 | 10671420 | 10694606 | - | mRNA | protein_coding |
| 276576 | enst00000379586 | sg00000137434 | c6orf52-202 | 6 | 10671422 | 10694609 | - | mRNA | protein_coding |
| 276764 | enst00000503680 | sg00000137434 | c6orf52-206 | 6 | 10671422 | 10694797 | - | mRNA | protein_coding |
| 276939 | enst00000379568 | sg00000111845 | pak1ip1-201 | 6 | 10694972 | 10709782 | + | mRNA | protein_coding |
| -298573 | enst00000401715 | sg00000216368 | al136226.1-201 | 6 | 10118452 | 10119253 | + | pseudogenic_transcript | processed_pseudogene |
| -302251 | enst00000485268 | sg00000181355 | ofcc1-210 | 6 | 9939289 | 10114774 | - | lnc_RNA | processed_transcript |
| 304882 | enst00000541412 | sg00000111843 | tmem14c-205 | 6 | 10722915 | 10731119 | + | mRNA | protein_coding |
| 305037 | enst00000229563 | sg00000111843 | tmem14c-201 | 6 | 10723070 | 10731127 | + | mRNA | protein_coding |
| 305076 | enst00000466421 | sg00000111843 | tmem14c-202 | 6 | 10723109 | 10730763 | + | lnc_RNA | processed_transcript |
| 305092 | enst00000467415 | sg00000111843 | tmem14c-203 | 6 | 10723125 | 10731129 | + | lnc_RNA | processed_transcript |
| 306389 | enst00000495549 | sg00000111843 | tmem14c-204 | 6 | 10724422 | 10728727 | + | lnc_RNA | processed_transcript |
| 329536 | enst00000606522 | sg00000272097 | al024498.1-201 | 6 | 10743324 | 10747569 | - | lnc_RNA | lncrna |
| 329586 | enst00000659819 | sg00000272097 | al024498.1-203 | 6 | 10743324 | 10747619 | - | lnc_RNA | lncrna |
| 329630 | enst00000606652 | sg00000272097 | al024498.1-202 | 6 | 10746953 | 10747663 | - | lnc_RNA | lncrna |
| 329726 | enst00000463448 | sg00000137210 | tmem14b-206 | 6 | 10747759 | 10852753 | + | mRNA | nonsense_mediated_decay |
| 329726 | enst00000473166 | sg00000137210 | tmem14b-209 | 6 | 10747759 | 10829186 | + | mRNA | nonsense_mediated_decay |
| 329726 | enst00000612333 | sg00000137210 | tmem14b-220 | 6 | 10747759 | 10756971 | + | mRNA | protein_coding |
| 329728 | enst00000460341 | sg00000137210 | tmem14b-203 | 6 | 10747761 | 10838617 | + | mRNA | nonsense_mediated_decay |
| 329740 | enst00000491103 | sg00000137210 | tmem14b-218 | 6 | 10747773 | 10756958 | + | lnc_RNA | processed_transcript |
| 329740 | enst00000480194 | sg00000137210 | tmem14b-214 | 6 | 10747773 | 10756615 | + | lnc_RNA | processed_transcript |
| 329761 | enst00000480294 | sg00000272162 | al024498.2-201 | 6 | 10747794 | 10930423 | + | mRNA | nonsense_mediated_decay |
| 329768 | enst00000473807 | sg00000137210 | tmem14b-211 | 6 | 10747801 | 10802536 | + | mRNA | nonsense_mediated_decay |
| 329772 | enst00000379542 | sg00000137210 | tmem14b-202 | 6 | 10747805 | 10756981 | + | mRNA | protein_coding |
| 329772 | enst00000475942 | sg00000137210 | tmem14b-212 | 6 | 10747805 | 10755810 | + | mRNA | protein_coding |
| 329772 | enst00000461342 | sg00000137210 | tmem14b-204 | 6 | 10747805 | 10755479 | + | mRNA | protein_coding |
| 329772 | enst00000492297 | sg00000137210 | tmem14b-219 | 6 | 10747805 | 10750036 | + | lnc_RNA | processed_transcript |
| 329778 | enst00000379530 | sg00000137210 | tmem14b-201 | 6 | 10747811 | 10756947 | + | mRNA | protein_coding |
| 329778 | enst00000463100 | sg00000137210 | tmem14b-205 | 6 | 10747811 | 10829165 | + | mRNA | nonsense_mediated_decay |
| 329784 | enst00000473276 | sg00000137210 | tmem14b-210 | 6 | 10747817 | 10756973 | + | mRNA | protein_coding |
| 329798 | enst00000481240 | sg00000137210 | tmem14b-215 | 6 | 10747831 | 10759684 | + | mRNA | protein_coding |
| 329798 | enst00000467317 | sg00000137210 | tmem14b-208 | 6 | 10747831 | 10759774 | + | mRNA | protein_coding |
| 331632 | enst00000478732 | sg00000137210 | tmem14b-213 | 6 | 10749665 | 10802410 | + | mRNA | nonsense_mediated_decay |
| 331931 | enst00000486421 | sg00000137210 | tmem14b-216 | 6 | 10749964 | 10756697 | + | lnc_RNA | processed_transcript |
| 333137 | enst00000467229 | sg00000137210 | tmem14b-207 | 6 | 10751170 | 10829205 | + | mRNA | nonsense_mediated_decay |
| 334893 | enst00000410451 | sg00000222383 | rna5sp203-201 | 6 | 10752791 | 10752926 | - | pseudogenic_transcript | rrna_pseudogene |
| 352044 | enst00000489137 | sg00000137210 | tmem14b-217 | 6 | 10770077 | 10829203 | + | lnc_RNA | processed_transcript |
| -356260 | enst00000472329 | sg00000181355 | ofcc1-208 | 6 | 9896711 | 10060765 | - | lnc_RNA | processed_transcript |
| 412846 | enst00000538030 | sg00000111837 | mak-205 | 6 | 10764201 | 10830879 | - | mRNA | protein_coding |
| 420462 | enst00000313243 | sg00000111837 | mak-201 | 6 | 10762723 | 10838495 | - | mRNA | protein_coding |
| 420498 | enst00000474039 | sg00000111837 | mak-203 | 6 | 10762723 | 10838531 | - | mRNA | protein_coding |
| 420522 | enst00000536370 | sg00000111837 | mak-204 | 6 | 10762740 | 10838555 | - | mRNA | protein_coding |
| 420522 | enst00000354489 | sg00000111837 | mak-202 | 6 | 10762740 | 10838555 | - | mRNA | protein_coding |
| -439426 | enst00000491508 | sg00000181355 | ofcc1-213 | 6 | 9900413 | 9977599 | - | lnc_RNA | processed_transcript |
| 463747 | enst00000436249 | sg00000235051 | al357497.1-201 | 6 | 10881780 | 10884349 | + | lnc_RNA | lncrna |
| 464008 | enst00000379491 | sg00000124827 | gcm2-201 | 6 | 10873223 | 10882041 | - | mRNA | protein_coding |
| 468798 | enst00000341041 | sg00000153157 | sycp2l-202 | 6 | 10886831 | 10974194 | + | mRNA | nonsense_mediated_decay |
| 469019 | enst00000283141 | sg00000153157 | sycp2l-201 | 6 | 10887052 | 10974309 | + | mRNA | protein_coding |
| 473474 | enst00000543878 | sg00000153157 | sycp2l-207 | 6 | 10891507 | 10963806 | + | mRNA | protein_coding |
| -477676 | enst00000460066 | sg00000181355 | ofcc1-201 | 6 | 9750251 | 9939349 | - | lnc_RNA | processed_transcript |
| -477676 | enst00000642964 | sg00000181355 | ofcc1-216 | 6 | 9596297 | 9939349 | - | pseudogenic_transcript | transcribed_unitary_pseudogene |
| -477697 | enst00000492094 | sg00000181355 | ofcc1-214 | 6 | 9596290 | 9939328 | - | lnc_RNA | processed_transcript |
| -477697 | enst00000466385 | sg00000181355 | ofcc1-204 | 6 | 9896866 | 9939328 | - | lnc_RNA | processed_transcript |
| -477706 | enst00000460363 | sg00000181355 | ofcc1-202 | 6 | 9707762 | 9939319 | - | lnc_RNA | processed_transcript |
| 479981 | enst00000487561 | sg00000153157 | sycp2l-205 | 6 | 10898014 | 10924584 | + | mRNA | nonsense_mediated_decay |
| -483736 | enst00000486246 | sg00000181355 | ofcc1-211 | 6 | 9840322 | 9933289 | - | lnc_RNA | processed_transcript |
| -483744 | enst00000469426 | sg00000181355 | ofcc1-206 | 6 | 9809745 | 9933281 | - | lnc_RNA | processed_transcript |
| -483744 | enst00000487015 | sg00000181355 | ofcc1-212 | 6 | 9705425 | 9933281 | - | lnc_RNA | processed_transcript |
| -483758 | enst00000492169 | sg00000181355 | ofcc1-215 | 6 | 9707933 | 9933267 | - | 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