Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000087576-chr19-+-22971474-22972800 l44 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 926845 reads mapping to 331194 Unique genomic coordinates Making up 9052 groups Consisting of 2725 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000042755-chr5-+-90924490-90925701 l43 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 666475 reads mapping to 334423 Unique genomic coordinates Making up 9220 groups Consisting of 2671 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000172010-chr19-+-22935793-22936902 l44 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 874881 reads mapping to 370700 Unique genomic coordinates Making up 10026 groups Consisting of 3084 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028600-chr2---104333605-104334603 l45 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 971076 reads mapping to 350080 Unique genomic coordinates Making up 9322 groups Consisting of 2887 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000038845-chr3---106569745-106572404 l45 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 805226 reads mapping to 365460 Unique genomic coordinates Making up 9989 groups Consisting of 3083 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039894-chr13---14131305-14131905 l44 e 5 nr 1000000 chr ENSMUST00000156124-chr4-+-10819910-10821005 l43 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1197313 reads mapping to 365241 Unique genomic coordinates Making up 9934 groups Consisting of 2931 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000150459-chr10-+-83224163-83225506 l44 e 6 nr 1000000 chr ENSMUST00000169423-chr4---150450186-150451206 l45 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1217347 reads mapping to 342781 Unique genomic coordinates Making up 9233 groups Consisting of 2691 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000020927-chr12-+-8330176-8331407 l42 e 7 nr 1000000 chr ENSMUST00000159504-chr7-+-96954657-96958707 l43 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1109246 reads mapping to 359830 Unique genomic coordinates Making up 9734 groups Consisting of 2941 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029759-chr3---123071215-123073108 l45 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 974021 reads mapping to 346078 Unique genomic coordinates Making up 9451 groups Consisting of 2829 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000016640-chr19-+-29446444-29447509 l44 e 9 nr 1000000 chr ENSMUST00000084787-chr9---119522139-119523409 l45 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1036192 reads mapping to 352529 Unique genomic coordinates Making up 9538 groups Consisting of 2959 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138374-chr3---107821212-107825010 l45 e 10 nr 1000000 chr ENSMUST00000050887-chr6---87528587-87532410 l43 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1118994 reads mapping to 338345 Unique genomic coordinates Making up 9197 groups Consisting of 2741 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000134901-chr4-+-98186934-98188111 l43 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 849422 reads mapping to 353416 Unique genomic coordinates Making up 9451 groups Consisting of 2990 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173181-chr17-+-37386420-37387812 l44 e 12 nr 1000000 chr ENSMUST00000167014-chr9---86717723-86720412 l43 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1128955 reads mapping to 364110 Unique genomic coordinates Making up 9633 groups Consisting of 2910 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110624-chr2---121165987-121169813 l45 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 796482 reads mapping to 361945 Unique genomic coordinates Making up 9778 groups Consisting of 2975 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169794-chr3-+-59813892-59815114 l43 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 843843 reads mapping to 362226 Unique genomic coordinates Making up 9762 groups Consisting of 2985 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000123730-chr2-+-156585681-156588515 l45 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 932620 reads mapping to 370466 Unique genomic coordinates Making up 9952 groups Consisting of 3117 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000117341-chr3-+-54929956-54933616 l43 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 868038 reads mapping to 356995 Unique genomic coordinates Making up 9581 groups Consisting of 2981 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025215-chr18---35476996-35478117 l44 e 17 nr 1000000 chr ENSMUST00000173313-chr7-+-149182294-149183417 l45 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1150677 reads mapping to 365190 Unique genomic coordinates Making up 9882 groups Consisting of 3019 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000111955-chr14-+-34132889-34133618 l44 e 18 nr 1000000 chr ENSMUST00000164898-chr5---124847921-124849018 l45 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1207528 reads mapping to 360609 Unique genomic coordinates Making up 9736 groups Consisting of 3043 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102476-chr2-+-121976109-121978819 l45 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 894884 reads mapping to 368181 Unique genomic coordinates Making up 9969 groups Consisting of 2994 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098761-chr3-+-105470498-105476920 l45 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 792118 reads mapping to 338281 Unique genomic coordinates Making up 9137 groups Consisting of 2791 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000115263-chr18-+-61278106-61279221 l44 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 824908 reads mapping to 330332 Unique genomic coordinates Making up 8945 groups Consisting of 2735 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107398-chr11---100300854-100303122 l46 e 22 nr 1000000 chr ENSMUST00000148081-chr4---120440198-120440822 l45 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1414364 reads mapping to 361979 Unique genomic coordinates Making up 9841 groups Consisting of 3059 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169497-chr3-+-88706179-88707523 l43 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 722411 reads mapping to 361555 Unique genomic coordinates Making up 9736 groups Consisting of 2954 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024887-chr17-+-79340909-79344924 l44 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 845215 reads mapping to 365666 Unique genomic coordinates Making up 9943 groups Consisting of 2971 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000041865-chr2-+-68998627-68999725 l43 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 847180 reads mapping to 347710 Unique genomic coordinates Making up 9412 groups Consisting of 2834 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039631-chr19---34318902-34321726 l44 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 882943 reads mapping to 372239 Unique genomic coordinates Making up 10089 groups Consisting of 3015 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000090775-chr3---96091725-96092727 l43 e 27 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 705119 reads mapping to 341870 Unique genomic coordinates Making up 9189 groups Consisting of 2788 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000127217-chr18---70297818-70301228 l44 e 28 nr 1000000 chr ENSMUST00000070980-chr7---138288861-138289828 l45 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1151188 reads mapping to 350892 Unique genomic coordinates Making up 9544 groups Consisting of 2840 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000037181-chr12---68321457-68323529 l44 e 29 nr 1000000 chr ENSMUST00000023450-chr16-+-17335758-17337729 l44 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1407729 reads mapping to 348481 Unique genomic coordinates Making up 9284 groups Consisting of 2783 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000000687-chr17---84245477-84246130 l44 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 905937 reads mapping to 369585 Unique genomic coordinates Making up 10064 groups Consisting of 3067 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000145614-chr2-+-130389478-130394431 l45 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 851655 reads mapping to 373453 Unique genomic coordinates Making up 9868 groups Consisting of 2957 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000047023-chr4-+-84738041-84739232 l43 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 748610 reads mapping to 348500 Unique genomic coordinates Making up 9466 groups Consisting of 2863 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000119131-chr16-+-94615442-94618233 l44 e 33 nr 1000000 chr ENSMUST00000044165-chr9-+-118515808-118516733 l45 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1024424 reads mapping to 357790 Unique genomic coordinates Making up 9700 groups Consisting of 2896 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135296-chr2---32907116-32908234 l43 e 34 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 811153 reads mapping to 351182 Unique genomic coordinates Making up 9498 groups Consisting of 2867 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000152836-chr2---132629943-132633235 l45 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 851126 reads mapping to 355980 Unique genomic coordinates Making up 9735 groups Consisting of 2922 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000050715-chr19---17660000-17661136 l44 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 892453 reads mapping to 358402 Unique genomic coordinates Making up 9710 groups Consisting of 2960 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000141162-chr4---63937085-63937637 l43 e 37 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 709129 reads mapping to 345704 Unique genomic coordinates Making up 9365 groups Consisting of 2840 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000097352-chr17-+-31741198-31744638 l44 e 38 nr 1000000 chr ENSMUST00000057645-chrX---54749845-54755538 l43 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1014199 reads mapping to 347908 Unique genomic coordinates Making up 9411 groups Consisting of 2832 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167204-chr3-+-55269995-55275239 l43 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 797612 reads mapping to 358304 Unique genomic coordinates Making up 9734 groups Consisting of 2913 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000052695-chr2-+-127035930-127038640 l45 e 40 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 807096 reads mapping to 351504 Unique genomic coordinates Making up 9632 groups Consisting of 2896 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000096029-chr19---46391644-46392341 l44 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 876224 reads mapping to 369961 Unique genomic coordinates Making up 10006 groups Consisting of 2970 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000131418-chr4---80927105-80931442 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 723776 reads mapping to 337443 Unique genomic coordinates Making up 9246 groups Consisting of 2719 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000010007-chr4-+-140521910-140523043 l45 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 690954 reads mapping to 358186 Unique genomic coordinates Making up 9753 groups Consisting of 2896 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000172193-chr2-+-91608572-91609744 l43 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 785268 reads mapping to 353713 Unique genomic coordinates Making up 9614 groups Consisting of 2830 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107231-chr3---94877415-94878545 l43 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 805184 reads mapping to 365323 Unique genomic coordinates Making up 9750 groups Consisting of 2960 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000153772-chr2-+-69560602-69561846 l43 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 912173 reads mapping to 365211 Unique genomic coordinates Making up 9882 groups Consisting of 2973 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000168614-chr2---9784222-9785347 l41 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 793278 reads mapping to 347148 Unique genomic coordinates Making up 9458 groups Consisting of 2854 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030471-chr4-+-115766982-115769648 l45 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 690656 reads mapping to 348690 Unique genomic coordinates Making up 9549 groups Consisting of 2912 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161371-chr10-+-122322764-122323349 l46 e 49 nr 1000000 chr ENSMUST00000116488-chr14---46087677-46089549 l44 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1478679 reads mapping to 357506 Unique genomic coordinates Making up 9757 groups Consisting of 2986 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028817-chr2---132076480-132079050 l45 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 979188 reads mapping to 362205 Unique genomic coordinates Making up 9825 groups Consisting of 3013 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000027560-chr18-+-62571326-62572451 l44 e 51 nr 1000000 chr ENSMUST00000101670-chrX-+-23380395-23383151 l43 e 51 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1361683 reads mapping to 337551 Unique genomic coordinates Making up 9192 groups Consisting of 2791 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000131082-chr3---116393304-116398052 l45 e 52 nr 1000000 chr ENSMUST00000063635-chr5---143026434-143027052 l45 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1213896 reads mapping to 370550 Unique genomic coordinates Making up 9990 groups Consisting of 3074 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163105-chr3---135762745-135764053 l45 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 763387 reads mapping to 362541 Unique genomic coordinates Making up 9777 groups Consisting of 2964 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000077200-chr2---135912629-135913754 l45 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 748598 reads mapping to 367667 Unique genomic coordinates Making up 9971 groups Consisting of 2998 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000049714-chr11-+-83832362-83833955 l44 e 55 nr 1000000 chr ENSMUST00000049714-chr11-+-83832362-83833955 l44 e 55 nr 1500000 chr ENSMUST00000112061-chr6---129590914-129593355 l45 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1598127 reads mapping to 344837 Unique genomic coordinates Making up 9333 groups Consisting of 2758 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028278-chr2-+-61601394-61603556 l43 e 56 nr 1000000 chr ENSMUST00000034987-chr9-+-86417331-86418456 l43 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1147024 reads mapping to 361767 Unique genomic coordinates Making up 9608 groups Consisting of 3000 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125478-chr3---87979273-87980357 l43 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 755145 reads mapping to 367927 Unique genomic coordinates Making up 10003 groups Consisting of 3112 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165396-chr3---27393354-27398258 l43 e 58 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 817426 reads mapping to 340437 Unique genomic coordinates Making up 9215 groups Consisting of 2802 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026480-chr4---106339601-106341359 l45 e 59 nr 1000000 chr ENSMUST00000168164-chr8---13104275-13105459 l43 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1183800 reads mapping to 346895 Unique genomic coordinates Making up 9479 groups Consisting of 2934 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098534-chr3-+-145239172-145240460 l45 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 855558 reads mapping to 346835 Unique genomic coordinates Making up 9378 groups Consisting of 2903 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109054-chr2---174991756-174996461 l45 e 61 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 779751 reads mapping to 349303 Unique genomic coordinates Making up 9393 groups Consisting of 2942 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022875-chr15-+-27482944-27484062 l44 e 62 nr 1000000 chr ENSMUST00000117227-chr7-+-86576500-86580762 l43 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1149156 reads mapping to 358879 Unique genomic coordinates Making up 9711 groups Consisting of 2830 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102960-chr2-+-13995727-13996463 l43 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 928503 reads mapping to 345299 Unique genomic coordinates Making up 9377 groups Consisting of 2792 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000002805-chr2-+-145736909-145738764 l45 e 64 nr 1000000 chr ENSMUST00000112691-chrX---147433740-147436164 l45 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1006719 reads mapping to 361207 Unique genomic coordinates Making up 9790 groups Consisting of 2972 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000129708-chr3-+-108074709-108075965 l45 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 895256 reads mapping to 344686 Unique genomic coordinates Making up 9278 groups Consisting of 2735 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169338-chr7-+-29767073-29769666 l43 e 66 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 574567 reads mapping to 313777 Unique genomic coordinates Making up 8531 groups Consisting of 2478 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135974-chr2---146310357-146311467 l45 e 67 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 745327 reads mapping to 354936 Unique genomic coordinates Making up 9618 groups Consisting of 2970 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000120739-chr2---81962674-81963268 l43 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 852893 reads mapping to 363900 Unique genomic coordinates Making up 9906 groups Consisting of 2932 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029551-chr3-+-89867847-89872269 l43 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 945670 reads mapping to 337253 Unique genomic coordinates Making up 9229 groups Consisting of 2665 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102518-chr4-+-137460485-137461570 l45 e 70 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 730217 reads mapping to 330423 Unique genomic coordinates Making up 9114 groups Consisting of 2761 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000112616-chr2-+-57887110-57888271 l43 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 818171 reads mapping to 349387 Unique genomic coordinates Making up 9558 groups Consisting of 2856 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000120408-chr2---177715239-177716372 l45 e 72 nr 1000000 chr ENSMUST00000035078-chr9-+-111125270-111128172 l45 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1032127 reads mapping to 363120 Unique genomic coordinates Making up 9782 groups Consisting of 3039 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000103224-chr2---126654246-126657573 l45 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 767213 reads mapping to 352541 Unique genomic coordinates Making up 9626 groups Consisting of 2921 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163724-chr2-+-152395074-152395274 l45 e 74 nr 1000000 chr ENSMUST00000122983-chr8---17392091-17393174 l43 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1112088 reads mapping to 359653 Unique genomic coordinates Making up 9707 groups Consisting of 2920 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022601-chr14---79879680-79881075 l44 e 75 nr 1000000 chr ENSMUST00000075806-chr16---29260503-29261575 l44 e 75 nr 1500000 chr ENSMUST00000172791-chr2---12041074-12042175 l43 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1826117 reads mapping to 354469 Unique genomic coordinates Making up 9659 groups Consisting of 2939 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028178-chr2---58147837-58149076 l43 e 76 nr 1000000 chr ENSMUST00000028178-chr2---58147837-58149076 l43 e 76 nr 1500000 chr ENSMUST00000028178-chr2---58147837-58149076 l43 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1924947 reads mapping to 342497 Unique genomic coordinates Making up 9214 groups Consisting of 2757 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000134292-chr5---107330906-107333877 l45 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 767908 reads mapping to 346230 Unique genomic coordinates Making up 9366 groups Consisting of 2852 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000097504-chr18---82779497-82780578 l44 e 78 nr 1000000 chr ENSMUST00000097504-chr18---82779497-82780578 l44 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1488263 reads mapping to 383021 Unique genomic coordinates Making up 10269 groups Consisting of 3175 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028392-chr2-+-80158817-80159979 l43 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 787564 reads mapping to 347933 Unique genomic coordinates Making up 9581 groups Consisting of 2850 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000128334-chr18---10009351-10010580 l44 e 80 nr 1000000 chr ENSMUST00000165771-chr7---93376190-93380280 l43 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1207370 reads mapping to 365151 Unique genomic coordinates Making up 9853 groups Consisting of 3035 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028233-chr2---34894231-34895781 l43 e 81 nr 1000000 chr ENSMUST00000112334-chrX---159080706-159081581 l45 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1015634 reads mapping to 340573 Unique genomic coordinates Making up 9265 groups Consisting of 2801 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000072835-chr18---46470848-46471582 l44 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 893504 reads mapping to 364037 Unique genomic coordinates Making up 9811 groups Consisting of 3009 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000064244-chr2---26809083-26812383 l43 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 823733 reads mapping to 365850 Unique genomic coordinates Making up 9840 groups Consisting of 2977 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000152002-chr5---67021296-67022384 l43 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 706958 reads mapping to 334887 Unique genomic coordinates Making up 9125 groups Consisting of 2676 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165341-chr10---107207096-107209885 l46 e 85 nr 1000000 chr ENSMUST00000075299-chr18---61559444-61560085 l44 e 85 nr 1500000 chr ENSMUST00000016294-chrX---39995253-39996485 l43 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1531793 reads mapping to 363212 Unique genomic coordinates Making up 9625 groups Consisting of 2978 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000065634-chr19---7860372-7861586 l42 e 86 nr 1000000 chr ENSMUST00000066041-chr7---4785332-4786486 l41 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1476784 reads mapping to 364402 Unique genomic coordinates Making up 9802 groups Consisting of 3012 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102735-chr2-+-62162282-62164787 l43 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 935828 reads mapping to 369724 Unique genomic coordinates Making up 9998 groups Consisting of 3026 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170492-chr3-+-34536091-34536688 l43 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 835136 reads mapping to 354538 Unique genomic coordinates Making up 9506 groups Consisting of 2892 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030452-chr4-+-116381114-116383389 l45 e 89 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 705987 reads mapping to 335575 Unique genomic coordinates Making up 8925 groups Consisting of 2796 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025968-chr19-+-39634849-39635990 l44 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 984860 reads mapping to 344852 Unique genomic coordinates Making up 9219 groups Consisting of 2860 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000151984-chr2-+-60207550-60209291 l43 e 91 nr 1000000 chr ENSMUST00000113658-chr6-+-87034746-87042191 l43 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1244546 reads mapping to 359475 Unique genomic coordinates Making up 9849 groups Consisting of 2909 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 1000000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 1500000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 2000000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 2500000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 3000000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 3500000 chr ENSMUST00000105647-chr4-+-151932937-151937292 l45 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 3717212 reads mapping to 346802 Unique genomic coordinates Making up 9333 groups Consisting of 2821 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102899-chr2---26760782-26765093 l43 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 885566 reads mapping to 366526 Unique genomic coordinates Making up 9950 groups Consisting of 3054 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170632-chr4-+-99581685-99582894 l43 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 822837 reads mapping to 373218 Unique genomic coordinates Making up 9973 groups Consisting of 2988 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000074195-chr3---144367977-144370195 l45 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 729472 reads mapping to 343031 Unique genomic coordinates Making up 9255 groups Consisting of 2825 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000111110-chr2---104844582-104847496 l45 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 921883 reads mapping to 365714 Unique genomic coordinates Making up 9931 groups Consisting of 3122 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107157-chr4---86629028-86637997 l43 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 910640 reads mapping to 346424 Unique genomic coordinates Making up 9295 groups Consisting of 2914 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028351-chr2-+-24823905-24825698 l43 e 98 nr 1000000 chr ENSMUST00000014421-chr5---90691784-90695098 l43 e 98 nr 1500000 chr ENSMUST00000033437-chrX---46406386-46407598 l43 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1517040 reads mapping to 359929 Unique genomic coordinates Making up 9603 groups Consisting of 2966 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000103135-chr2-+-156328881-156330099 l45 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 832632 reads mapping to 347041 Unique genomic coordinates Making up 9369 groups Consisting of 2707 clusters