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
#114 6 3224545 3225483 938 3 37 7.56115e-17 6.59611e-15
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
2170 enst00000259818 sg00000137285 tubb2b-201 6 3224277 3227653 - mRNA protein_coding
5920 enst00000509933 sg00000180822 psmg4-210 6 3231403 3270835 + mRNA nonsense_mediated_decay
6247 enst00000473006 sg00000137285 tubb2b-202 6 3224283 3231730 - lnc_RNA processed_transcript
6324 enst00000380306 sg00000180822 psmg4-203 6 3231807 3267781 + mRNA protein_coding
6346 enst00000416079 sg00000180822 psmg4-204 6 3231829 3237865 + lnc_RNA processed_transcript
-28761 enst00000656983 sg00000230269 linc02525-203 6 3182626 3195784 - lnc_RNA lncrna
-28761 enst00000435043 sg00000230269 linc02525-202 6 3182626 3195784 - lnc_RNA lncrna
-28761 enst00000425384 sg00000230269 linc02525-201 6 3182630 3195784 - lnc_RNA lncrna
33411 enst00000438998 sg00000180822 psmg4-206 6 3258894 3268049 + mRNA protein_coding
33414 enst00000380305 sg00000180822 psmg4-202 6 3258897 3267779 + mRNA protein_coding
33469 enst00000419065 sg00000180822 psmg4-205 6 3258952 3267781 + mRNA protein_coding
33478 enst00000473000 sg00000180822 psmg4-209 6 3258961 3268050 + mRNA protein_coding
33494 enst00000324987 sg00000180822 psmg4-201 6 3258977 3267920 + mRNA nonsense_mediated_decay
33501 enst00000451246 sg00000180822 psmg4-207 6 3258984 3303373 + mRNA protein_coding
33577 enst00000454610 sg00000180822 psmg4-208 6 3259060 3291984 + mRNA protein_coding
-44781 enst00000404155 sg00000216819 tubb2bp1-201 6 3177044 3179764 - pseudogenic_transcript unprocessed_pseudogene
58637 enst00000482874 sg00000137266 slc22a23-208 6 3273356 3284120 - lnc_RNA retained_intron
-67001 enst00000333628 sg00000137267 tubb2a-201 6 3153666 3157544 - mRNA protein_coding
-67019 enst00000489942 sg00000137267 tubb2a-202 6 3154579 3157526 - lnc_RNA processed_transcript
-71483 enst00000447644 sg00000228170 al031963.1-201 6 3138394 3153062 - lnc_RNA lncrna
-74531 enst00000464040 sg00000137274 bphl-209 6 3150014 3153046 + lnc_RNA processed_transcript
-84120 enst00000423798 sg00000137274 bphl-204 6 3140425 3153028 + mRNA protein_coding
86179 enst00000607565 sg00000272320 al445309.1-201 6 3311662 3313650 + lnc_RNA lncrna
-97749 enst00000488487 sg00000137274 bphl-211 6 3126796 3152533 + lnc_RNA retained_intron
98682 enst00000433689 sg00000137266 slc22a23-204 6 3323342 3324165 - lnc_RNA processed_transcript
98700 enst00000467144 sg00000137266 slc22a23-206 6 3286984 3324183 - lnc_RNA processed_transcript
-105219 enst00000380375 sg00000137274 bphl-202 6 3119326 3152669 + mRNA protein_coding
-105737 enst00000380368 sg00000137274 bphl-201 6 3118808 3138083 + mRNA protein_coding
-105817 enst00000479273 sg00000137274 bphl-210 6 3118728 3124143 + lnc_RNA retained_intron
-105819 enst00000490918 sg00000137274 bphl-212 6 3118726 3153062 + lnc_RNA retained_intron
-105834 enst00000380379 sg00000137274 bphl-203 6 3118711 3153578 + mRNA protein_coding
-105853 enst00000433912 sg00000137274 bphl-207 6 3118692 3152645 + mRNA nonsense_mediated_decay
-106169 enst00000430655 sg00000137274 bphl-206 6 3118376 3153195 + mRNA nonsense_mediated_decay
-106169 enst00000424847 sg00000137274 bphl-205 6 3118376 3152669 + mRNA nonsense_mediated_decay
-106171 enst00000434640 sg00000137274 bphl-208 6 3118374 3152575 + mRNA protein_coding
-135736 enst00000410316 sg00000222248 rna5sp201-201 6 3088686 3088809 - pseudogenic_transcript rrna_pseudogene
-147721 enst00000380409 sg00000137275 ripk1-202 6 3076824 3115187 + mRNA protein_coding
152503 enst00000496753 sg00000137266 slc22a23-211 6 3289766 3377986 - lnc_RNA processed_transcript
-155651 enst00000606441 sg00000272277 al031963.3-201 6 3068045 3068894 - lnc_RNA lncrna
-156051 enst00000259808 sg00000137275 ripk1-201 6 3068494 3115187 + mRNA protein_coding
-160554 enst00000479389 sg00000137275 ripk1-203 6 3063991 3106051 + lnc_RNA processed_transcript
-168696 enst00000433761 sg00000229282 al031963.2-201 6 3055849 3057357 + lnc_RNA lncrna
-175710 enst00000401898 sg00000217707 serpinb8p1-201 6 3048835 3049211 + pseudogenic_transcript unprocessed_pseudogene
-179161 enst00000428729 sg00000232654 fam136bp-201 6 3045384 3045800 + pseudogenic_transcript processed_pseudogene
-191362 enst00000612789 sg00000274855 al133351.3-201 6 3033183 3033288 + pseudogenic_transcript processed_pseudogene
-200773 enst00000604204 sg00000271361 htatsf1p2-201 6 3023142 3023772 - pseudogenic_transcript processed_pseudogene
213935 enst00000467177 sg00000137266 slc22a23-207 6 3283874 3439418 - mRNA protein_coding
219486 enst00000497691 sg00000137266 slc22a23-212 6 3271774 3444969 - mRNA nonsense_mediated_decay
219501 enst00000490273 sg00000137266 slc22a23-210 6 3272830 3444984 - mRNA protein_coding
219530 enst00000380302 sg00000137266 slc22a23-202 6 3271774 3445013 - mRNA protein_coding
-220378 enst00000606474 sg00000124588 nqo2-209 6 3004167 3010189 + mRNA protein_coding
-224387 enst00000380430 sg00000124588 nqo2-202 6 3000158 3019762 + mRNA protein_coding
-224543 enst00000380454 sg00000124588 nqo2-204 6 3000002 3019755 + mRNA protein_coding
-224556 enst00000380441 sg00000124588 nqo2-203 6 2999989 3019755 + mRNA protein_coding
-224571 enst00000338130 sg00000124588 nqo2-201 6 2999974 3019762 + mRNA protein_coding
-224651 enst00000380455 sg00000124588 nqo2-205 6 2999894 3028869 + mRNA protein_coding
-224669 enst00000397717 sg00000124588 nqo2-207 6 2999876 3015643 + mRNA protein_coding
-224941 enst00000660868 sg00000224846 nqo2-as1-204 6 2989336 2999604 - lnc_RNA lncrna
-225368 enst00000665347 sg00000224846 nqo2-as1-205 6 2989726 2999177 - lnc_RNA lncrna
-225411 enst00000429319 sg00000224846 nqo2-as1-201 6 2989726 2999134 - lnc_RNA lncrna
-225739 enst00000658240 sg00000224846 nqo2-as1-203 6 2989335 2998806 - lnc_RNA lncrna
-225802 enst00000456189 sg00000224846 nqo2-as1-202 6 2989722 2998743 - lnc_RNA lncrna
230560 enst00000485307 sg00000137266 slc22a23-209 6 3283465 3456043 - mRNA protein_coding
231076 enst00000380298 sg00000137266 slc22a23-201 6 3323342 3456559 - mRNA protein_coding
231076 enst00000406686 sg00000137266 slc22a23-203 6 3269458 3456559 - mRNA protein_coding
231539 enst00000436008 sg00000137266 slc22a23-205 6 3268962 3457022 - mRNA protein_coding
-235887 enst00000454015 sg00000244041 linc01011-203 6 2988658 2990252 + lnc_RNA lncrna
-235897 enst00000605901 sg00000244041 linc01011-204 6 2988648 2991173 + lnc_RNA lncrna
-235899 enst00000380472 sg00000124588 nqo2-206 6 2988646 3015643 + mRNA protein_coding
-236558 enst00000426637 sg00000124588 nqo2-208 6 2987987 3012561 + mRNA protein_coding
-236578 enst00000450238 sg00000244041 linc01011-202 6 2987967 2990348 + lnc_RNA lncrna
-236578 enst00000445000 sg00000244041 linc01011-201 6 2987967 2991173 + lnc_RNA lncrna
-252380 enst00000616722 sg00000124570 serpinb6-207 6 2948171 2972165 - mRNA protein_coding
-252768 enst00000646775 sg00000124570 serpinb6-223 6 2954703 2971777 - mRNA protein_coding
-252884 enst00000380520 sg00000124570 serpinb6-201 6 2948196 2971661 - mRNA protein_coding
-252901 enst00000644388 sg00000124570 serpinb6-213 6 2948193 2971644 - mRNA protein_coding
-252940 enst00000643098 sg00000124570 serpinb6-209 6 2948159 2971605 - mRNA protein_coding
-252960 enst00000380546 sg00000124570 serpinb6-205 6 2948159 2971585 - mRNA protein_coding
-252978 enst00000380539 sg00000124570 serpinb6-204 6 2948159 2971567 - mRNA protein_coding
-253191 enst00000645421 sg00000124570 serpinb6-219 6 2955605 2971354 - mRNA protein_coding
-253214 enst00000643227 sg00000124570 serpinb6-210 6 2955605 2971331 - mRNA protein_coding
-253261 enst00000646688 sg00000124570 serpinb6-221 6 2955652 2971284 - mRNA protein_coding
-253269 enst00000642543 sg00000124570 serpinb6-208 6 2948175 2971276 - mRNA protein_coding
-253275 enst00000644693 sg00000124570 serpinb6-214 6 2948245 2971270 - mRNA nonsense_mediated_decay
-253307 enst00000644777 sg00000124570 serpinb6-216 6 2955655 2971238 - mRNA protein_coding
-253339 enst00000380529 sg00000124570 serpinb6-203 6 2948159 2971206 - mRNA protein_coding
-253497 enst00000612421 sg00000124570 serpinb6-206 6 2948164 2971048 - mRNA protein_coding
-253800 enst00000649845 sg00000124570 serpinb6-225 6 2948162 2970745 - mRNA nonsense_mediated_decay
-253802 enst00000644178 sg00000124570 serpinb6-212 6 2948163 2970743 - mRNA protein_coding
-253831 enst00000645580 sg00000124570 serpinb6-220 6 2948217 2970714 - mRNA protein_coding
-260540 enst00000644828 sg00000124570 serpinb6-217 6 2948966 2964005 - mRNA protein_coding
-262406 enst00000644875 sg00000124570 serpinb6-218 6 2959298 2962139 - mRNA protein_coding
-262437 enst00000380524 sg00000124570 serpinb6-202 6 2948159 2962108 - mRNA protein_coding
-263218 enst00000643314 sg00000124570 serpinb6-211 6 2948159 2961327 - lnc_RNA retained_intron
-266376 enst00000647157 sg00000124570 serpinb6-224 6 2948164 2958169 - lnc_RNA retained_intron
-266957 enst00000646722 sg00000124570 serpinb6-222 6 2948160 2957588 - lnc_RNA retained_intron
-268663 enst00000644697 sg00000124570 serpinb6-215 6 2948170 2955882 - lnc_RNA retained_intron
-307651 enst00000437718 sg00000228365 al133351.1-201 6 2916894 2917733 + lnc_RNA lncrna
-312432 enst00000454998 sg00000232999 al133351.2-201 6 2910613 2912113 - pseudogenic_transcript unprocessed_pseudogene
-321236 enst00000380698 sg00000170542 serpinb9-201 6 2887270 2903309 - mRNA protein_coding
-343138 enst00000668503 sg00000230438 serpinb9p1-207 6 2854245 2881407 - lnc_RNA lncrna
-343252 enst00000665261 sg00000230438 serpinb9p1-205 6 2854245 2881293 - lnc_RNA lncrna
-343259 enst00000545177 sg00000230438 serpinb9p1-202 6 2854658 2881286 - lnc_RNA lncrna
-343259 enst00000667461 sg00000230438 serpinb9p1-206 6 2854575 2881286 - lnc_RNA lncrna
-347213 enst00000670827 sg00000230438 serpinb9p1-209 6 2854660 2877332 - lnc_RNA lncrna
-347938 enst00000670540 sg00000230438 serpinb9p1-208 6 2854220 2876607 - lnc_RNA lncrna
-347992 enst00000654948 sg00000230438 serpinb9p1-203 6 2854202 2876553 - lnc_RNA lncrna
-348028 enst00000661223 sg00000230438 serpinb9p1-204 6 2851230 2876517 - lnc_RNA lncrna
-348028 enst00000420981 sg00000230438 serpinb9p1-201 6 2854659 2876517 - lnc_RNA lncrna
-370438 enst00000583158 sg00000266750 mir4645-201 6 2854031 2854107 - miRNA mirna
373643 enst00000660471 sg00000228793 al033523.1-214 6 3593578 3599126 - lnc_RNA lncrna
-382586 enst00000490094 sg00000021355 serpinb1-205 6 2835856 2841959 - lnc_RNA processed_transcript
-382682 enst00000380739 sg00000021355 serpinb1-201 6 2832332 2841863 - mRNA protein_coding
-382683 enst00000460260 sg00000021355 serpinb1-202 6 2838549 2841862 - lnc_RNA processed_transcript
-382697 enst00000476896 sg00000021355 serpinb1-204 6 2836108 2841848 - lnc_RNA processed_transcript
-386546 enst00000468511 sg00000021355 serpinb1-203 6 2833512 2837999 - lnc_RNA processed_transcript
399264 enst00000443445 sg00000228793 al033523.1-201 6 3593848 3624747 - lnc_RNA lncrna
428107 enst00000652961 sg00000228793 al033523.1-228 6 3593657 3653590 - lnc_RNA lncrna
428242 enst00000667419 sg00000228793 al033523.1-223 6 3593657 3653725 - lnc_RNA lncrna
-455772 enst00000380764 sg00000124535 wrnip1-201 6 2768773 2785745 + mRNA protein_coding
-458493 enst00000380769 sg00000124535 wrnip1-202 6 2766052 2786952 + mRNA protein_coding
-459113 enst00000618555 sg00000124535 wrnip1-205 6 2765432 2785744 + mRNA protein_coding
-459131 enst00000380771 sg00000124535 wrnip1-203 6 2765414 2785745 + mRNA protein_coding
-459152 enst00000380773 sg00000124535 wrnip1-204 6 2765393 2786952 + mRNA protein_coding
468592 enst00000605153 sg00000270477 al033523.2-201 6 3693923 3694075 - pseudogenic_transcript processed_pseudogene
-473623 enst00000274643 sg00000145949 mylk4-201 6 2663637 2750922 - mRNA protein_coding
-480397 enst00000647417 sg00000145949 mylk4-202 6 2663629 2744148 - mRNA protein_coding
493986 enst00000661070 sg00000228793 al033523.1-215 6 3593587 3719469 - lnc_RNA lncrna
494126 enst00000661196 sg00000228793 al033523.1-209 6 3588702 3719609 - lnc_RNA lncrna
494160 enst00000655990 sg00000228793 al033523.1-233 6 3631783 3719643 - lnc_RNA lncrna
494196 enst00000663773 sg00000228793 al033523.1-226 6 3593657 3719679 - lnc_RNA lncrna
494337 enst00000653626 sg00000228793 al033523.1-235 6 3662795 3719820 - lnc_RNA lncrna
494337 enst00000658658 sg00000228793 al033523.1-205 6 3585193 3719820 - lnc_RNA lncrna
494504 enst00000670704 sg00000228793 al033523.1-217 6 3593587 3719987 - lnc_RNA lncrna
494557 enst00000668872 sg00000228793 al033523.1-225 6 3593657 3720040 - lnc_RNA lncrna
494565 enst00000656112 sg00000228793 al033523.1-232 6 3594348 3720048 - lnc_RNA lncrna
494586 enst00000661957 sg00000228793 al033523.1-221 6 3593640 3720069 - lnc_RNA lncrna
494590 enst00000668915 sg00000228793 al033523.1-206 6 3585241 3720073 - lnc_RNA lncrna
494594 enst00000667255 sg00000228793 al033523.1-216 6 3593587 3720077 - lnc_RNA lncrna
494594 enst00000659072 sg00000228793 al033523.1-234 6 3652413 3720077 - lnc_RNA lncrna
494594 enst00000668020 sg00000228793 al033523.1-208 6 3588665 3720077 - lnc_RNA lncrna
494594 enst00000669421 sg00000228793 al033523.1-210 6 3588756 3720077 - lnc_RNA lncrna
494594 enst00000669829 sg00000228793 al033523.1-231 6 3593776 3720077 - lnc_RNA lncrna
494594 enst00000662672 sg00000228793 al033523.1-230 6 3593669 3720077 - lnc_RNA lncrna
494594 enst00000665671 sg00000228793 al033523.1-227 6 3593657 3720077 - lnc_RNA lncrna
494594 enst00000660793 sg00000228793 al033523.1-229 6 3593657 3720077 - lnc_RNA lncrna
494594 enst00000659450 sg00000228793 al033523.1-213 6 3593553 3720077 - lnc_RNA lncrna
494594 enst00000657929 sg00000228793 al033523.1-222 6 3593657 3720077 - lnc_RNA lncrna
494594 enst00000653557 sg00000228793 al033523.1-211 6 3593497 3720077 - lnc_RNA lncrna
494594 enst00000660734 sg00000228793 al033523.1-202 6 3593505 3720077 - lnc_RNA lncrna
494594 enst00000655328 sg00000228793 al033523.1-212 6 3593513 3720077 - lnc_RNA lncrna
494594 enst00000665760 sg00000228793 al033523.1-204 6 3585101 3720077 - lnc_RNA lncrna
494594 enst00000667691 sg00000228793 al033523.1-220 6 3593633 3720077 - lnc_RNA lncrna
494594 enst00000669021 sg00000228793 al033523.1-219 6 3593627 3720077 - lnc_RNA lncrna
494594 enst00000661016 sg00000228793 al033523.1-218 6 3593627 3720077 - lnc_RNA lncrna
494594 enst00000656179 sg00000228793 al033523.1-224 6 3593657 3720077 - lnc_RNA lncrna
494594 enst00000662974 sg00000228793 al033523.1-207 6 3588605 3720077 - lnc_RNA lncrna
494598 enst00000666680 sg00000228793 al033523.1-203 6 3593490 3720081 - 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