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 100000 45175 46099 8726 0 1452797 46768 152252 6688 292234 35838 919017 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 46064 44273 9663 0 1432969 51586 136387 7144 284339 42020 911493 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 46023 44177 9800 0 1422622 48507 146646 7359 281287 36057 902766 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 44720 46252 9028 0 1403354 46955 144123 6874 277989 35540 891873 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 43312 48071 8617 0 1376795 43381 155884 6798 275311 33605 861816 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 46211 44326 9463 0 1451901 48860 148228 7255 288741 35386 923431 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 45267 45725 9008 0 1438388 49666 148192 7185 286858 36215 910272 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 45304 45437 9259 0 1420514 49009 146686 7303 282255 31447 903814 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 44931 44230 10839 0 1349942 48334 137052 7736 268288 39216 849316 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 44649 45046 10305 0 1358832 45450 141733 7070 271660 33845 859074 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 44232 46581 9187 0 1381007 49547 137979 6872 275631 35045 875933 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 44751 46156 9093 0 1398966 48723 143551 7205 276654 36788 886045 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 41068 49558 9374 0 1280490 51142 126971 6347 263380 50412 782238 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 40472 50750 8778 0 1258945 49975 118253 6498 253146 45498 785575 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 41270 48908 9822 0 1259492 46766 127922 6696 257823 54175 766110 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 38638 52838 8524 0 1187602 45245 113591 5749 240273 46056 736688 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 43035 47180 9785 0 1328729 51781 126344 7253 268067 52915 822369 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 39588 49429 10983 0 1160580 43784 116615 6484 236254 46612 710831 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 36420 54154 9426 0 1076985 37941 107393 5651 216779 42826 666395 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 37601 51813 10586 0 1090879 38872 108363 5795 222063 45688 670098 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 43638 47451 8911 0 1380393 50036 132885 8693 279697 53232 855850 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 40710 50349 8941 0 1288250 47707 130095 6030 266530 50534 787354 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 41120 47679 11201 0 1210712 45834 121772 6782 247802 54452 734070 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam 100000 37834 51480 10686 0 1096629 38504 113366 5942 223121 42344 673352 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 42105 48599 9296 0 1299008 48249 129776 6347 262940 50137 801559 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 38642 52857 8501 0 1182642 42228 125051 5395 238162 32535 739271 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 40708 50747 8545 0 1285492 49369 129234 6583 262943 42294 795069 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 42517 48281 9202 0 1331400 47146 130388 6629 268941 40870 837426 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 42466 47104 10430 0 1283864 48464 126521 6495 264415 46806 791163 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 39426 51455 9119 0 1211193 43601 125087 6566 251433 53458 731048 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 43685 46277 10038 0 1347498 56000 129714 7287 277021 48471 829005 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 40447 47066 12487 0 1138212 41493 117465 6520 229470 42401 700863 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 41523 46402 12075 0 1184436 46818 116014 6259 239367 47129 728849 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 43422 47401 9177 0 1371773 56309 128701 6811 279332 50466 850154 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 41233 47638 11129 0 1207297 51102 114819 6936 244162 57304 732974 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam 100000 42882 44164 12954 0 1220982 50023 114797 6998 247337 51803 750024 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 39958 46562 13480 0 1097117 45280 111878 6524 221485 51112 660838 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 43502 43133 13365 0 1251141 50142 127409 7138 259611 52714 754127 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 40167 45914 13919 0 1115719 39515 114348 6616 231412 44418 679410 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 42840 46070 11090 0 1290862 51956 132069 6869 265339 47541 787088 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 41477 48589 9934 0 1257148 46335 126604 6389 255163 43971 778686 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 43486 43666 12848 0 1267261 55024 119794 7467 257247 51124 776605 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 42752 46595 10653 0 1288026 50434 126689 7171 262459 49935 791338 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 43957 43157 12886 0 1257487 51006 121319 7464 256081 49314 772303 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 43302 46830 9868 0 1345209 54864 128231 7262 272857 53779 828216 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 44661 43895 11444 0 1329207 53928 126519 7314 269265 51209 820972 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 41917 46925 11158 0 1242008 48297 127128 6642 255980 50565 753396 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam 100000 39562 49720 10718 0 1138403 44328 115184 5844 230009 44270 698768 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 42172 45818 12010 0 1224292 52008 115136 6689 246587 49368 754504 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 45739 41246 13015 0 1314425 58632 120145 7688 264343 57277 806340 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 46044 41743 12213 0 1338618 56405 126578 6815 269457 48427 830936 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam 100000 45423 41318 13259 0 1290068 59321 117391 7220 257855 48280 800001