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 chgs Unmethylated chgs Methylated CHHs Unmethylated CHHs EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam 20349659 9095591 9572011 1682056 1 1259755 7835836 183501406 6658001 18809270 852229 36884209 1574350 118723347 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam 30015261 13633935 13665400 2715925 1 2020190 11613745 256681996 10137100 24263858 1260299 51430750 2323535 167266454 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam 27014996 12312882 12235438 2466675 1 1846060 10466822 231214858 8681437 22978618 1156157 46067897 1936920 150393829 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam 26302191 11581685 12489960 2230545 1 1726942 9854743 224084049 8423482 22028913 1104529 44713152 1867274 145946699 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam 28905983 12331886 14292877 2281217 3 1918064 10413822 243953258 8558544 25838202 1135855 48531203 2017566 157871888 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam 24140505 11050080 10973461 2116961 3 1579974 9470106 217946429 8187042 21761145 1062536 43433409 1832611 141669686 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam 22262118 9986594 10417464 1858059 1 1536515 8450079 196938082 7564205 19544907 967557 39233900 1694338 127933175 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam 24557803 11023910 11430018 2103873 2 1723786 9300124 215109906 8244675 21307910 1071477 42824701 1772832 139888311 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam 28731808 12720630 13210078 2801099 1 2161126 10559504 225992948 9046557 21842118 1202237 45361388 2001278 146539370 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam 27792315 12229033 12912342 2650939 1 1939155 10289878 222520026 8205504 22514794 1105916 44690621 1849444 144153747 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam 21160872 9316818 10036514 1807539 1 1420739 7896079 180013500 6934397 17647358 872844 35893215 1579087 117086599 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam 25314513 11191274 11992514 2130723 2 1835341 9355933 214985786 8245428 21238566 1047240 42806098 1811240 139837214 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam 24505793 9915441 12555282 2035069 1 2705164 7210277 154371720 6619617 14863708 739999 32156644 1943298 98048454 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam 29855018 11727816 15750735 2376467 0 3318046 8409770 181742375 7874020 16740253 929405 36920601 2251146 117026950 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam 26009397 10439071 13324084 2246240 2 3739516 6699555 136016129 5750945 13021245 699624 28351144 1733351 86459820 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam 25226760 9405544 13904236 1916980 0 2636021 6769523 142831749 5958725 13541358 672814 29209282 1876297 91573273 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam 15453987 6380873 7739907 1333207 0 1736608 4644265 99137282 4217985 9196803 535634 20037165 1932988 63216707 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam 31922572 12255648 16675995 2990928 1 3263582 8992066 176538868 7344361 16933790 912079 36262599 2297548 112788491 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam 24510805 8593705 13929047 1988051 2 2262879 6330826 124508835 4903316 12097133 619102 25334277 1795108 79759899 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam 22769546 8267039 12467371 2035136 0 1883875 6383164 122908719 4824979 12090566 612515 25238601 1827593 78314465 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam 24481250 10438000 12046563 1996687 0 2802912 7635088 169475057 6721143 15986854 1081552 34252524 3482873 107950111 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam 22688467 8967128 11891374 1829965 0 2474742 6492386 139836026 5749134 13380784 652679 28960958 1958750 89133721 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam 21392200 8408055 10932504 2051637 4 1984624 6423431 127237948 5351229 12254820 663359 26439097 2095978 80433465 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam 27996279 10233760 15243065 2519447 7 2436682 7797078 151781122 5915753 15089108 746213 31172597 1797219 97060232 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam 24654280 10209529 12327982 2116768 1 2284909 7924620 169230320 6854838 16729782 805593 34594121 2153742 108092244 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam 36345555 13724717 19810124 2810707 7 3630031 10094686 212732771 8409431 21389527 937010 42655847 2366691 136974265 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam 27212918 10790980 14282015 2139922 1 2580715 8210265 182131746 7773669 17313389 910797 37265101 2287864 116580926 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam 31499315 13143700 15672601 2683014 0 2877178 10266522 222524486 8754862 21458168 1102130 44943458 2694418 143571450 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam 20689148 8444728 10305796 1938622 2 2148266 6296462 128398540 5213255 12567730 627120 26364706 2204316 81421413 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam 11003725 4103253 6008199 892273 0 1336980 2766273 57532394 2287343 5639671 323890 11658279 1768982 35854229 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam 22734395 9655530 10981695 2097166 4 2556625 7098905 150742463 6936899 13822954 814250 31050905 2156222 95961233 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam 21488138 8423410 10776872 2287855 1 2230577 6192833 115906900 4644294 11620008 619856 23551619 1638581 73832542 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam 26770469 10697352 13242455 2830662 0 2526429 8170923 156322050 6612365 15198462 770831 31981857 2168983 99589552 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam 27459153 11624042 13557404 2277707 0 2623096 9000946 203726589 8959141 18995825 996952 41660215 2787951 130326505 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam 15913069 6267321 8113691 1532057 0 1900244 4367077 88024093 4047323 8070663 479419 17975035 1871691 55579962 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam 25100695 10396121 11933311 2771262 1 2895134 7500987 143389134 6473128 13251440 794893 29375321 2249885 91244467 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam 16541499 6323590 8364655 1853251 3 1603675 4719915 85575964 3859626 8425101 469729 17659824 1198594 53963090 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam 20931018 8694087 9860951 2375978 2 1956411 6737676 128475689 5690111 12491913 686060 26714902 1836981 81055722 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam 29146503 11240945 14550345 3355209 4 2599604 8641341 158634154 6281105 16254051 854946 33112776 1753269 100378007 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam 29638248 12390014 14317340 2930889 5 3444505 8945509 181303125 8133825 17357263 907176 37254559 2249034 115401268 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam 28660043 11468068 14622941 2569028 6 2764190 8703878 181129898 7299763 17951668 895027 36965157 2311106 115707177 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam 21150005 8898557 9932657 2318790 1 2505655 6392902 126318223 5908942 11618123 702435 25937403 1841804 80309516 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam 15670592 6443740 7744109 1482742 1 2081383 4362357 89710026 3860035 8426280 483168 18264364 1807632 56868547 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam 16300374 6871475 7612342 1816555 2 1959853 4911622 96701418 4236787 9099073 538030 19735564 1814920 61277044 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam 11133150 4644692 5510557 977901 0 1206577 3438115 74285747 3347989 6780487 403265 15120311 1509605 47124090 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam 13531234 5777318 6365101 1388812 3 1567966 4209352 86316145 3751343 8102850 464615 17545411 1765502 54686424 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam 19891722 8020237 9946231 1925253 1 1983971 6036266 120448317 5162434 11661347 610621 24880747 1841547 76291621 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam 29439432 11206077 15456327 2777025 3 3923633 7282444 139950493 5977998 13704103 651184 28593233 1768421 89255554 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam 25055317 10110532 12402840 2541943 2 3711212 6399320 128539262 5867583 11862497 687621 26124666 2454676 81542219 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam 29623269 13173399 13088150 3361720 0 4597382 8576017 167743909 8085260 15228220 910439 34537608 2251034 106731348 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam 22573555 10112774 10003930 2456851 0 3692163 6420611 128026299 5689722 11970270 671794 25906277 2537937 81250299 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam 13762658 6084804 6118468 1559385 1 2053760 4031044 79983322 3855731 7250942 431899 16319796 1321843 50803111