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 zr1394_10_s456_trimmed_bismark_bt2.bam 78221457 25432383 21496817 31262071 30186 16497594 8934789 54706781 6634857 1559899 291620 10265526 4272996 31681883 zr1394_11_s456_trimmed_bismark_bt2.bam 54458572 15661567 16326025 22452404 18576 7483670 8177897 50769500 7110525 1619619 280561 9193433 3592530 28972832 zr1394_12_s456_trimmed_bismark_bt2.bam 59459431 20129239 17101979 22211756 16457 6468963 13660276 80756458 8385192 2342276 335216 15323134 5285129 49085511 zr1394_13_s456_trimmed_bismark_bt2.bam 64352550 19701041 18442450 26188891 20168 8466837 11234204 68890041 9111111 1824835 344677 12907020 4621384 40081014 zr1394_14_s456_trimmed_bismark_bt2.bam 87834637 25515667 26159848 36134252 24870 11084136 14431531 87759971 11235176 2398111 442616 15471847 5958507 52253714 zr1394_15_s456_trimmed_bismark_bt2.bam 67984205 19984905 20315504 27663637 20159 9182295 10802610 66776329 9440679 1675246 363316 12344351 4683749 38268988 zr1394_16_s456_trimmed_bismark_bt2.bam 74531056 21356588 22542289 30609163 23016 9432803 11923785 73264966 10020093 2096343 387586 13149191 5124999 42486754 zr1394_17_s456_trimmed_bismark_bt2.bam 42070546 12876923 12141296 17039733 12594 5030453 7846470 48108192 6661066 1196534 251010 9443102 3311685 27244795 zr1394_18_s456_trimmed_bismark_bt2.bam 55048106 18154684 15404219 21472931 16272 6050438 12104246 72146273 8198593 1888052 315055 13985858 4549990 43208725 zr1394_1_s456_trimmed_bismark_bt2.bam 46792286 14599936 13908254 18270707 13389 4336772 10263164 61540104 7261799 1790508 303140 11577501 3988762 36618394 zr1394_2_s456_trimmed_bismark_bt2.bam 46105140 14893041 13855099 17344092 12908 4549028 10344013 61756286 7131612 1653180 297938 11820461 4106610 36746485 zr1394_3_s456_trimmed_bismark_bt2.bam 48376729 14826395 14694166 18841972 14196 4320719 10505676 62586254 7108309 1714938 298530 11486929 4119726 37857822 zr1394_4_s456_trimmed_bismark_bt2.bam 44905078 13933186 13481308 17477962 12622 4353271 9579915 57797022 7147884 1323418 292457 10962379 3772656 34298228 zr1394_5_s456_trimmed_bismark_bt2.bam 47401736 15825610 13874948 17687993 13185 3966524 11859086 69420697 6725035 2383446 308623 13280520 4618857 42104216 zr1394_6_s456_trimmed_bismark_bt2.bam 46455148 15610896 13764452 17067657 12143 3712222 11898674 68879669 6320809 1817405 308317 12911503 4429364 43092271 zr1394_7_s456_trimmed_bismark_bt2.bam 49730113 15447299 14857626 19410370 14818 4681556 10765743 64930647 7871119 1765508 320635 12298987 4170941 38503457 zr1394_8_s456_trimmed_bismark_bt2.bam 38697189 12090076 11378609 15218243 10261 3553043 8537033 51677627 6649597 1131323 247967 9857922 3261945 30528873 zr1394_9_s456_trimmed_bismark_bt2.bam 77350922 25367884 21586770 30374506 21762 8687619 16680265 97723805 9596337 2711789 406190 17840843 6301142 60867504 zr1394_all_s456_trimmed_bismark_bt2.bam 605809374 185658855 176357696 243604381 188442 124261073 61397782 366293238 37861620 11160761 2119087 61988385 31889543 221273842