File Total Reads Aligned Reads Unaligned Reads Ambiguously Aligned Reads No Genomic Sequence Duplicate Reads (removed) Unique Reads (remaining) Total Cs Methylated CpGs Unmethylated CpGs Methylated CpHs Unmethylated CpHs Methylated CHHs Unmethylated CHHs EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam 20349659 12933060 3894864 3477633 44102 2202000 10731060 254979684 8382494 27227884 1214264 52651156 2969621 162534265 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam 30015261 18819411 5947034 5187377 61439 3289942 15529469 351339061 12585950 34494729 1754913 72316992 4334261 225852216 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam 27014996 16700962 5610754 4638124 65156 2902189 13798773 314149561 10722930 32227593 1570404 64160249 3455732 202012653 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam 26302191 16425059 5220361 4598538 58233 3210217 13214842 307540029 10454072 31616733 1517132 63030781 3203768 197717543 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam 28905983 17801176 6103503 4947190 54114 3686649 14114527 339132197 10734677 37931197 1595800 69174107 3556551 216139865 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam 24140505 15315195 4643634 4127848 53828 2626295 12688900 298191131 10186869 30850360 1462308 60956834 3226983 191507777 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam 22262118 14110653 4255255 3850216 45994 2690816 11419837 270599486 9458882 28031269 1348956 55284830 3125061 173350488 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam 24557803 15451363 4731553 4317319 57568 2999531 12451832 294499987 10264289 30413930 1467513 60119353 3101571 189133331 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam 28731808 17332078 6195835 5138393 65502 3597067 13735011 307325823 11088149 30941628 1618193 63320213 3589588 196768052 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam 27792315 16590771 6324163 4830166 47215 3134922 13455849 303674703 10129037 31784709 1503822 62614055 3235980 194407100 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam 21160872 12824444 4767792 3534609 34027 2239644 10584800 247046085 8640655 25088052 1218039 50493706 2998211 158607422 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam 25314513 15678404 5225438 4361523 49148 3148783 12529621 293934778 10252234 30288053 1441056 60017753 3195321 188740361 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam 24505793 14204942 6024162 4202384 74305 4313588 9891354 218397239 8227458 22623508 1129848 46785687 4352339 135278399 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam 29855018 16499291 8473853 4793870 88004 5114942 11384349 252522211 9762997 24585479 1376152 52613100 4893259 159291224 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam 26009397 14957895 6426460 4519302 105740 5875438 9082457 192380687 7109547 19918475 1052940 41381397 3712462 119205866 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam 25226760 13267422 8094344 3771491 93503 4091356 9176066 199949327 7378911 20067707 1045578 41845846 4525832 125085453 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam 15453987 9081303 3665126 2652399 55159 2742296 6339007 141773876 5263088 13743929 901988 28802830 5990258 87071783 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam 31922572 16691335 9758658 5364152 108427 4980013 11711322 246513535 8951340 25233290 1370402 51865829 5350906 153741768 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam 24510805 11759160 9041136 3656525 53984 3445175 8313985 173661827 5988422 17801995 957457 35915413 4610416 108388124 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam 22769546 11112785 8105839 3487565 63357 2821038 8291747 171709280 5870357 17680991 959986 35876377 4831755 106489814 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam 24481250 14896437 5375378 4122905 86530 4386955 10509482 239595329 8422219 23743599 1686608 49285780 7882265 148574858 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam 22688467 13137265 5593168 3877026 81008 4109932 9027333 201153808 7229421 20834329 1051010 42690769 5004469 124343810 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam 21392200 11640293 5987742 3714284 49881 3116295 8523998 181234560 6570532 18666360 1073337 38271453 5780399 110872479 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam 27996279 13917954 9517105 4470817 90403 3882364 10035590 210743690 7165620 22368692 1092035 44317346 3929059 131870938 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam 24654280 14423415 6060084 4102431 68350 3699607 10723808 236933033 8490018 24686337 1229473 49573983 5166186 147787036 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam 36345555 19526957 11086969 5585191 146438 6093978 13432979 295683002 10357251 31870324 1395892 60641867 4964362 186453306 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam 27212918 15686974 6927718 4503470 94756 4456475 11230499 256492616 9677056 26122561 1372992 53795074 5234750 160290183 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam 31499315 18577099 7572690 5230711 118815 4814378 13762721 309081863 10856396 31126499 1626460 63867452 6108488 195496568 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam 20689148 11777721 5355311 3461806 94310 3400697 8377024 182659399 6423527 18733650 1047628 37912742 6582803 111959049 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam 11003725 6124376 3011158 1822658 45533 2201339 3923037 88246998 2920391 9078127 659983 17480450 6679533 51428514 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam 22734395 13511277 5092561 4068412 62145 3984035 9527242 211868934 8582613 20778524 1241231 44591913 5319278 131355375 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam 21488138 10921771 6944690 3565429 56248 3214011 7707760 159956992 5547539 16909179 918082 33025440 4109531 99447221 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam 26770469 13850429 8441595 4400929 77516 3604979 10245450 215212165 7915273 22018432 1169495 44851717 5383679 133873569 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam 27459153 16538141 6266029 4571301 83682 4182646 12355495 286889268 11184609 28372501 1543016 59958991 6825308 179004843 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam 15913069 8505647 4729683 2632693 45046 2679573 5826074 126873753 5001166 12308526 837366 25946432 6015853 76764410 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam 25100695 13470954 7236216 4319816 73709 3956750 9514204 198582575 7805045 19110541 1222811 41405150 6058079 122980949 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam 16541499 8085337 5658467 2754391 43304 2287403 5797934 118376493 4570560 12573772 700456 24922800 2921486 72687419 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam 20931018 11475974 5600370 3808728 45946 2987985 8487989 179909756 6840587 18905942 1043615 38214194 4576293 110329125 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam 29146503 14321289 9939248 4779902 106064 3855826 10465463 216163363 7448449 23171580 1186371 46394787 3378233 134583943 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam 29638248 16992612 7251197 5327486 66953 5344954 11647658 252178148 9898616 26128046 1353513 53152959 4966379 156678635 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam 28660043 15730938 8230323 4621821 76961 4327800 11403138 251139371 8929513 26181990 1338652 52343352 5553563 156792301 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam 21150005 11600087 5775467 3715934 58517 3506517 8093570 174479557 7121333 17011312 1049286 36507272 4659213 108131141 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam 15670592 8919143 3965068 2740480 45901 3084323 5834820 129326626 4785260 12777350 836412 26383374 5952112 78592118 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam 16300374 8942620 4456627 2853713 47414 2677909 6264711 136529341 5133920 13487431 875886 28017758 5525110 83489236 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam 11133150 6639172 2473880 1974617 45481 1925651 4713521 107029543 4183509 10323567 693539 21846524 4871254 65111150 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam 13531234 7704618 3471625 2325361 29630 2205404 5499214 122410899 4581698 11957770 783227 24873164 5602427 74612613 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam 19891722 11088022 5248262 3496939 58499 3127264 7960758 171078466 6324525 17780401 977619 35948078 5216805 104831038 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam 29439432 14915064 9760279 4682666 81423 5591422 9323642 194682345 7215577 20277098 1012353 40592876 4664377 120920064 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam 25055317 13451347 7395470 4125849 82651 5031715 8419632 184279574 7231139 17777822 1192911 37522164 8090852 112464686 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam 29623269 16878077 7361312 5324337 59543 5949512 10928565 230149373 9797001 21851850 1331538 48404322 5440340 143324322 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam 22573555 13055046 5488169 3976247 54093 4831602 8223444 179948249 6937231 17229670 1118919 36308078 8434136 109920215 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam 13762658 7701905 3651938 2377015 31800 2550122 5151783 111476725 4688440 10466395 693518 22907665 4172951 68547756