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 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam 9246318 3662558 1217825 4358543 7392 401216 3261342 18418940 711829 1765366 51116 3330611 941472 11618546 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam 11654467 4572578 1541276 5531435 9178 553860 4018718 22700735 857067 2181742 96044 4052616 1264268 14248998 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam 11555321 4549927 1568078 5428395 8921 576435 3973492 22418499 864057 2143790 58013 4055876 1131000 14165763 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam 11408856 4527463 1477731 5394965 8697 515221 4012242 22548787 885408 2132942 57876 4060404 1134467 14277690 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam 12231319 4788889 1651146 5781653 9631 605118 4183771 23636238 888785 2289596 69679 4274461 1224859 14888858 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam 12175584 4734709 1704908 5726339 9628 573306 4161403 23480080 856232 2288185 84715 4200647 1318449 14731852 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam 10113854 3976894 1329633 4799454 7873 403813 3573081 20116328 747346 1948285 49389 3629427 1010916 12730965 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam 13949213 5438263 1876942 6622932 11076 692232 4746031 26831960 930960 2680491 76720 4844288 1361218 16938283 zr1394_10_s456_trimmed_bismark_bt2.bam 78221457 26440742 19431424 32285804 63487 17149949 9290793 56744251 7001331 1610356 290718 10834457 4127690 32879699 zr1394_11_s456_trimmed_bismark_bt2.bam 54458572 16280360 15053965 23084041 40206 7765728 8514632 52745371 7496104 1672681 284680 9692391 3508788 30090727 zr1394_12_s456_trimmed_bismark_bt2.bam 59459431 20852667 15643544 22925333 37887 6676630 14176037 83579208 8817849 2417237 332971 16093330 5082422 50835399 zr1394_13_s456_trimmed_bismark_bt2.bam 64352550 20464081 16899806 26943572 45091 8773542 11690539 71524361 9602566 1879545 343395 13603952 4469957 41624946 zr1394_14_s456_trimmed_bismark_bt2.bam 87834637 26512507 24154445 37111009 56676 11489262 15023245 91128263 11844607 2469156 442638 16305886 5799842 54266134 zr1394_15_s456_trimmed_bismark_bt2.bam 67984205 20793846 18691846 28451956 46557 9547917 11245929 69372444 9956430 1720443 365258 13018203 4559022 39753088 zr1394_16_s456_trimmed_bismark_bt2.bam 74531056 22191399 20848664 31438528 52465 9778157 12413242 76091693 10560955 2162406 387693 13862536 4989670 44128433 zr1394_17_s456_trimmed_bismark_bt2.bam 42070546 13373055 11125453 17543071 28967 5209577 8163478 49945483 7022752 1231609 249647 9955503 3189408 28296564 zr1394_18_s456_trimmed_bismark_bt2.bam 55048106 18831950 14051321 22127687 37148 6252025 12579925 74777179 8630550 1943000 313258 14709809 4368376 44812186 zr1394_1_s456_trimmed_bismark_bt2.bam 46792286 15141400 12808090 18811670 31126 4480374 10661026 63766237 7639492 1844078 303268 12172751 3843218 37963430 zr1394_2_s456_trimmed_bismark_bt2.bam 46105140 15412092 12775552 17888173 29323 4686184 10725908 63871790 7486629 1699430 297475 12401334 3960155 38026767 zr1394_3_s456_trimmed_bismark_bt2.bam 48376729 15387182 13562727 19394676 32144 4468769 10918413 64869693 7482953 1764271 298257 12085494 3975661 39263057 zr1394_4_s456_trimmed_bismark_bt2.bam 44905078 14451278 12422799 18001138 29863 4498133 9953145 59900779 7516564 1356230 292784 11524663 3643159 35567379 zr1394_5_s456_trimmed_bismark_bt2.bam 47401736 16372339 12742540 18256765 30092 4080089 12292250 71751999 7066746 2460275 307446 13930216 4433156 43554160 zr1394_6_s456_trimmed_bismark_bt2.bam 46455148 16168840 12629511 17627828 28969 3828258 12340582 71229852 6643663 1870268 308396 13553335 4254229 44599961 zr1394_7_s456_trimmed_bismark_bt2.bam 49730113 16017969 13690949 19988660 32535 4832407 11185562 67296159 8280867 1816175 320066 12931899 4022598 39924554 zr1394_8_s456_trimmed_bismark_bt2.bam 38697189 12549888 10453397 15668737 25167 3674487 8875401 53598027 6996767 1160532 247134 10373161 3143493 31676940 zr1394_9_s456_trimmed_bismark_bt2.bam 77350922 26296063 19712667 31292909 49283 8969760 17326303 101202142 10096631 2793392 405216 18757453 6066529 63082921