Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000021331-chr12---66043427-66045100 l44 e 0 nr 1000000 chr ENSMUST00000110667-chr8---25703065-25704400 l43 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1060453 reads mapping to 359761 Unique genomic coordinates Making up 9603 groups Consisting of 2833 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000038010-chr2---25649379-25651301 l43 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 904349 reads mapping to 365934 Unique genomic coordinates Making up 9808 groups Consisting of 2883 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113532-chr2-+-31266269-31271302 l43 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 912059 reads mapping to 407935 Unique genomic coordinates Making up 10721 groups Consisting of 3198 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028536-chr2---106802684-106806303 l45 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 828240 reads mapping to 373407 Unique genomic coordinates Making up 9990 groups Consisting of 3008 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025228-chr18---34800250-34801804 l44 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 984175 reads mapping to 393540 Unique genomic coordinates Making up 10237 groups Consisting of 3100 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023497-chr16-+-33087688-33088805 l44 e 5 nr 1000000 chr ENSMUST00000034033-chr8-+-77972593-77973405 l43 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1057187 reads mapping to 396035 Unique genomic coordinates Making up 10489 groups Consisting of 3049 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000000904-chr16-+-18543704-18545806 l44 e 6 nr 1000000 chr ENSMUST00000046288-chr17-+-31657060-31657706 l44 e 6 nr 1500000 chr ENSMUST00000139851-chr9-+-28005525-28007106 l43 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1552593 reads mapping to 377826 Unique genomic coordinates Making up 10058 groups Consisting of 3025 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000162830-chr15---47832513-47833707 l44 e 7 nr 1000000 chr ENSMUST00000095830-chr6---67401791-67403007 l43 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1197144 reads mapping to 386368 Unique genomic coordinates Making up 10289 groups Consisting of 3057 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109443-chr2---161347726-161356808 l45 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 925991 reads mapping to 371423 Unique genomic coordinates Making up 9877 groups Consisting of 2904 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142696-chr2---60531502-60532609 l43 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 825134 reads mapping to 365206 Unique genomic coordinates Making up 9653 groups Consisting of 2939 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000162086-chr13-+-63999342-64001610 l44 e 10 nr 1000000 chr ENSMUST00000108495-chr7-+-17411313-17412510 l43 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1124193 reads mapping to 372801 Unique genomic coordinates Making up 9826 groups Consisting of 3006 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035840-chr2---84541990-84543111 l43 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 876981 reads mapping to 367530 Unique genomic coordinates Making up 9868 groups Consisting of 2896 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000146409-chr18---61352573-61359812 l44 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 946728 reads mapping to 390908 Unique genomic coordinates Making up 10371 groups Consisting of 3045 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169083-chr13---104633037-104634213 l46 e 13 nr 1000000 chr ENSMUST00000159574-chr13-+-104918809-104919913 l46 e 13 nr 1500000 chr ENSMUST00000165089-chr18-+-23791219-23792913 l44 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1920338 reads mapping to 391408 Unique genomic coordinates Making up 10407 groups Consisting of 3077 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000011934-chr2---76779379-76788714 l43 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 896085 reads mapping to 393243 Unique genomic coordinates Making up 10403 groups Consisting of 3090 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133163-chr2-+-30225315-30228415 l43 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 896438 reads mapping to 388735 Unique genomic coordinates Making up 10344 groups Consisting of 3005 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000154150-chr16---13844928-13846016 l44 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 915731 reads mapping to 375048 Unique genomic coordinates Making up 9882 groups Consisting of 3000 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148084-chr2-+-80463000-80465017 l43 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 945151 reads mapping to 398365 Unique genomic coordinates Making up 10572 groups Consisting of 3227 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107163-chr11-+-101903786-101905118 l46 e 18 nr 1000000 chr ENSMUST00000171613-chr6---3668065-3669218 l41 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1327051 reads mapping to 383829 Unique genomic coordinates Making up 10218 groups Consisting of 3044 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000168911-chr16---55815253-55820319 l44 e 19 nr 1000000 chr ENSMUST00000115057-chrX---41718635-41721519 l43 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1048565 reads mapping to 406405 Unique genomic coordinates Making up 10683 groups Consisting of 3168 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125627-chr4-+-95675493-95676720 l43 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 737948 reads mapping to 366369 Unique genomic coordinates Making up 9708 groups Consisting of 2975 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148309-chr2---168119866-168120621 l45 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 770710 reads mapping to 362210 Unique genomic coordinates Making up 9572 groups Consisting of 2807 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000059787-chr18-+-20759314-20763022 l44 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 918034 reads mapping to 381350 Unique genomic coordinates Making up 10085 groups Consisting of 3004 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167716-chr19-+-24010408-24012623 l44 e 23 nr 1000000 chr ENSMUST00000149771-chr9-+-100755716-100756823 l45 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1028192 reads mapping to 385484 Unique genomic coordinates Making up 10226 groups Consisting of 2994 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000115099-chr2-+-3035654-3036424 l41 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 873316 reads mapping to 395763 Unique genomic coordinates Making up 10556 groups Consisting of 3178 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000001339-chr1---188544857-188545925 l45 e 25 nr 1000000 chr ENSMUST00000118042-chr17---73539598-73541025 l44 e 25 nr 1500000 chr ENSMUST00000034912-chr9-+-89864691-89866425 l43 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1551885 reads mapping to 379870 Unique genomic coordinates Making up 10063 groups Consisting of 2921 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166560-chr13---48687355-48688526 l44 e 26 nr 1000000 chr ENSMUST00000080403-chr7-+-69521865-69526526 l43 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1258446 reads mapping to 400270 Unique genomic coordinates Making up 10673 groups Consisting of 3208 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026322-chr14---25273292-25277027 l44 e 27 nr 1000000 chr ENSMUST00000034228-chr8-+-97193721-97198327 l43 e 27 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1277284 reads mapping to 369153 Unique genomic coordinates Making up 9742 groups Consisting of 2891 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000038364-chr3-+-76423902-76424928 l43 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 941475 reads mapping to 375540 Unique genomic coordinates Making up 10082 groups Consisting of 2901 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000112745-chr2-+-48954737-48955829 l43 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 918343 reads mapping to 369058 Unique genomic coordinates Making up 9877 groups Consisting of 2877 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170804-chr12---105938075-105939230 l46 e 30 nr 1000000 chr ENSMUST00000147505-chr5---139605961-139606530 l45 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1132866 reads mapping to 394977 Unique genomic coordinates Making up 10526 groups Consisting of 3127 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136153-chr2-+-129433369-129434731 l45 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 842676 reads mapping to 392506 Unique genomic coordinates Making up 10458 groups Consisting of 3128 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000019913-chr10-+-34327112-34331032 l44 e 32 nr 1000000 chr ENSMUST00000169627-chr15-+-101934461-101946832 l46 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1486287 reads mapping to 385084 Unique genomic coordinates Making up 10123 groups Consisting of 3013 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113537-chr19-+-6097154-6098233 l42 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 870197 reads mapping to 384047 Unique genomic coordinates Making up 10206 groups Consisting of 2986 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000146190-chr13-+-63959039-63960134 l44 e 34 nr 1000000 chr ENSMUST00000115588-chr9-+-15523577-15525734 l43 e 34 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1246365 reads mapping to 373164 Unique genomic coordinates Making up 9886 groups Consisting of 2981 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000174015-chr17-+-22206925-22208135 l44 e 35 nr 1000000 chr ENSMUST00000112863-chrX-+-140225278-140232335 l45 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1009458 reads mapping to 396470 Unique genomic coordinates Making up 10462 groups Consisting of 3186 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099490-chr13-+-55377384-55379536 l44 e 36 nr 1000000 chr ENSMUST00000170437-chr7-+-75333959-75335536 l43 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1159982 reads mapping to 379373 Unique genomic coordinates Making up 10091 groups Consisting of 2954 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000164954-chr3---32380764-32381937 l43 e 37 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 823807 reads mapping to 366003 Unique genomic coordinates Making up 9702 groups Consisting of 2892 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114787-chr16---37115028-37116638 l44 e 38 nr 1000000 chr ENSMUST00000150436-chr6---149016072-149017738 l45 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1178250 reads mapping to 363043 Unique genomic coordinates Making up 9591 groups Consisting of 2821 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025864-chr19-+-5601873-5603439 l42 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 953236 reads mapping to 390785 Unique genomic coordinates Making up 10379 groups Consisting of 3103 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000146690-chr2-+-50405627-50406840 l43 e 40 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 929954 reads mapping to 382804 Unique genomic coordinates Making up 10333 groups Consisting of 3017 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039205-chr17-+-80582032-80584441 l44 e 41 nr 1000000 chr ENSMUST00000166190-chr7-+-83469410-83470541 l43 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1106658 reads mapping to 404235 Unique genomic coordinates Making up 10724 groups Consisting of 3043 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000140238-chr2-+-101902712-101905242 l45 e 42 nr 1000000 chr ENSMUST00000058771-chr7-+-74370250-74373342 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1106016 reads mapping to 373003 Unique genomic coordinates Making up 9826 groups Consisting of 2978 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029030-chr2-+-174606883-174609543 l45 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 787056 reads mapping to 385907 Unique genomic coordinates Making up 10343 groups Consisting of 3119 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000051605-chr2-+-125082085-125084344 l45 e 44 nr 1000000 chr ENSMUST00000147360-chr9-+-55961537-55963444 l43 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1071608 reads mapping to 377196 Unique genomic coordinates Making up 10082 groups Consisting of 3017 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000017348-chr11-+-98526870-98528445 l44 e 45 nr 1000000 chr ENSMUST00000127006-chr2-+-167431181-167433345 l45 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1364059 reads mapping to 392388 Unique genomic coordinates Making up 10418 groups Consisting of 3076 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000052927-chr2-+-158521098-158522446 l45 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 833914 reads mapping to 398033 Unique genomic coordinates Making up 10583 groups Consisting of 3124 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029461-chr3-+-99888720-99889847 l43 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 726123 reads mapping to 365955 Unique genomic coordinates Making up 9933 groups Consisting of 2879 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098143-chr4-+-40946218-40947248 l43 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 880694 reads mapping to 375773 Unique genomic coordinates Making up 9905 groups Consisting of 2991 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000053570-chr11-+-11387174-11389149 l44 e 49 nr 1000000 chr ENSMUST00000112395-chr2-+-65698088-65699249 l43 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1345374 reads mapping to 388630 Unique genomic coordinates Making up 10183 groups Consisting of 2972 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000044622-chr18-+-78229164-78231750 l44 e 50 nr 1000000 chr ENSMUST00000058744-chr7---110787646-110788750 l45 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1091539 reads mapping to 387006 Unique genomic coordinates Making up 10248 groups Consisting of 3053 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029741-chr3---96530772-96531551 l43 e 51 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 809155 reads mapping to 358458 Unique genomic coordinates Making up 9535 groups Consisting of 2805 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000120603-chr2---79001186-79001752 l43 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 978935 reads mapping to 393354 Unique genomic coordinates Making up 10409 groups Consisting of 3068 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107508-chr11-+-98490161-98491753 l44 e 53 nr 1000000 chr ENSMUST00000109731-chr2---154161116-154161853 l45 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1404884 reads mapping to 389319 Unique genomic coordinates Making up 10352 groups Consisting of 3099 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000112366-chr2---66137181-66138354 l43 e 54 nr 1000000 chr ENSMUST00000043609-chr7-+-140862549-140864654 l45 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1174741 reads mapping to 389509 Unique genomic coordinates Making up 10542 groups Consisting of 3103 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028162-chr2-+-32251416-32253755 l43 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 844485 reads mapping to 372882 Unique genomic coordinates Making up 9942 groups Consisting of 2933 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000078748-chr3---10331734-10335656 l43 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 802727 reads mapping to 383924 Unique genomic coordinates Making up 10203 groups Consisting of 3088 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000112984-chr19---11709801-11710857 l44 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 843525 reads mapping to 393006 Unique genomic coordinates Making up 10490 groups Consisting of 3122 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109822-chr11---5800823-5803758 l42 e 58 nr 1000000 chr ENSMUST00000068175-chr17-+-80736109-80737158 l44 e 58 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1499205 reads mapping to 369393 Unique genomic coordinates Making up 9823 groups Consisting of 2918 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000084354-chr4-+-111471175-111472359 l45 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 726184 reads mapping to 366204 Unique genomic coordinates Making up 9793 groups Consisting of 2891 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000164242-chr17-+-35660891-35664160 l44 e 60 nr 1000000 chr ENSMUST00000114470-chr6---50243326-50247660 l43 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1185683 reads mapping to 373186 Unique genomic coordinates Making up 9864 groups Consisting of 2969 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000132669-chr2---173414123-173416461 l45 e 61 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 906174 reads mapping to 377232 Unique genomic coordinates Making up 10010 groups Consisting of 2990 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000115314-chr16-+-24978779-24992662 l44 e 62 nr 1000000 chr ENSMUST00000080329-chr9-+-39269018-39269962 l43 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1045275 reads mapping to 393917 Unique genomic coordinates Making up 10319 groups Consisting of 3064 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142296-chr2---181305066-181306863 l45 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 773670 reads mapping to 374806 Unique genomic coordinates Making up 10025 groups Consisting of 3017 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000011733-chr17-+-56132766-56133864 l44 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 903811 reads mapping to 393508 Unique genomic coordinates Making up 10469 groups Consisting of 3051 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000101432-chr12-+-54601521-54602765 l44 e 65 nr 1000000 chr ENSMUST00000026126-chr7-+-104665632-104666765 l45 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1166844 reads mapping to 371798 Unique genomic coordinates Making up 10028 groups Consisting of 2921 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000151786-chr5---136653997-136657866 l45 e 66 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 667749 reads mapping to 338135 Unique genomic coordinates Making up 8913 groups Consisting of 2618 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026217-chr19---44160898-44163767 l44 e 67 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 945060 reads mapping to 376206 Unique genomic coordinates Making up 10051 groups Consisting of 3045 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000149383-chr2-+-34262291-34262868 l43 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 941654 reads mapping to 399360 Unique genomic coordinates Making up 10587 groups Consisting of 3165 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028282-chr2---27301099-27306569 l43 e 69 nr 1000000 chr ENSMUST00000050211-chr8---106764516-106765569 l45 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1049025 reads mapping to 372972 Unique genomic coordinates Making up 9897 groups Consisting of 2932 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026072-chr19-+-57546689-57547770 l44 e 70 nr 1000000 chr ENSMUST00000040826-chr6-+-6988354-6991770 l41 e 70 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1128530 reads mapping to 366733 Unique genomic coordinates Making up 9675 groups Consisting of 2824 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000154794-chr3-+-83575462-83576071 l43 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 809047 reads mapping to 371735 Unique genomic coordinates Making up 9970 groups Consisting of 2960 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024599-chr17---12889691-12892672 l44 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 959086 reads mapping to 393209 Unique genomic coordinates Making up 10465 groups Consisting of 3077 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000061042-chr3---145707282-145708373 l45 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 904212 reads mapping to 368491 Unique genomic coordinates Making up 9848 groups Consisting of 2885 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000081275-chr18---7222044-7224174 l42 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 967935 reads mapping to 389079 Unique genomic coordinates Making up 10196 groups Consisting of 3017 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000122434-chr2---36936007-36937975 l43 e 75 nr 1000000 chr ENSMUST00000129612-chrX---71110456-71112875 l43 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1008415 reads mapping to 386612 Unique genomic coordinates Making up 10272 groups Consisting of 3134 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000038874-chr2---38921734-38931176 l43 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 950966 reads mapping to 365427 Unique genomic coordinates Making up 9631 groups Consisting of 2887 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142642-chr2---151774110-151775577 l45 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 843488 reads mapping to 378668 Unique genomic coordinates Making up 9989 groups Consisting of 2974 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000103182-chr2---131823481-131824578 l45 e 78 nr 1000000 chr ENSMUST00000142209-chr9-+-56459324-56462278 l43 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1047384 reads mapping to 402862 Unique genomic coordinates Making up 10678 groups Consisting of 3119 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022331-chr14---35405529-35411179 l44 e 79 nr 1000000 chr ENSMUST00000131623-chrX-+-155979687-155980379 l45 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1001976 reads mapping to 376382 Unique genomic coordinates Making up 9901 groups Consisting of 2904 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000149254-chr2-+-126860280-126863080 l45 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 794122 reads mapping to 383401 Unique genomic coordinates Making up 10448 groups Consisting of 3090 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163880-chr16---17682752-17683781 l44 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 980722 reads mapping to 365623 Unique genomic coordinates Making up 9730 groups Consisting of 2892 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029548-chr3-+-89972716-89975082 l43 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 808341 reads mapping to 386233 Unique genomic coordinates Making up 10303 groups Consisting of 3032 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000046157-chr3---27365797-27366883 l43 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 882187 reads mapping to 399327 Unique genomic coordinates Making up 10555 groups Consisting of 3136 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000154982-chr17---24247315-24248584 l44 e 84 nr 1000000 chr ENSMUST00000147242-chr2-+-156121765-156122984 l45 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1312386 reads mapping to 366241 Unique genomic coordinates Making up 9691 groups Consisting of 2899 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000044031-chr2-+-101468979-101472685 l45 e 85 nr 1000000 chr ENSMUST00000112433-chr5---111183916-111186285 l45 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1230944 reads mapping to 388608 Unique genomic coordinates Making up 10374 groups Consisting of 2987 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000018710-chr11---69756045-69760686 l44 e 86 nr 1000000 chr ENSMUST00000073787-chr4-+-138869519-138870986 l45 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1203499 reads mapping to 380167 Unique genomic coordinates Making up 10078 groups Consisting of 2994 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000060642-chr15-+-91529814-91531587 l44 e 87 nr 1000000 chr ENSMUST00000153151-chr2-+-113548828-113549887 l45 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1371017 reads mapping to 391087 Unique genomic coordinates Making up 10265 groups Consisting of 3073 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000095945-chr14---47866556-47868388 l44 e 88 nr 1000000 chr ENSMUST00000156662-chr6---142745862-142746988 l45 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1107668 reads mapping to 377884 Unique genomic coordinates Making up 9990 groups Consisting of 2949 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000151937-chr2---71181447-71182589 l43 e 89 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 807743 reads mapping to 362592 Unique genomic coordinates Making up 9646 groups Consisting of 2846 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114076-chr16---91068777-91069390 l44 e 90 nr 1000000 chr ENSMUST00000033625-chrX-+-135624724-135626790 l45 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1003100 reads mapping to 369951 Unique genomic coordinates Making up 9935 groups Consisting of 2897 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106623-chr11-+-113514718-113521191 l46 e 91 nr 1000000 chr ENSMUST00000147691-chr3-+-37130255-37131391 l43 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1322536 reads mapping to 402454 Unique genomic coordinates Making up 10686 groups Consisting of 3086 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000077960-chr17---36175354-36179692 l44 e 92 nr 1000000 chr ENSMUST00000094665-chr2---120100470-120101692 l45 e 92 nr 1500000 chr ENSMUST00000094665-chr2---120100470-120101692 l45 e 92 nr 2000000 chr ENSMUST00000159596-chr9---18271864-18274492 l43 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 2046347 reads mapping to 384757 Unique genomic coordinates Making up 10096 groups Consisting of 3064 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000072312-chr3-+-32831562-32836993 l43 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 862686 reads mapping to 387416 Unique genomic coordinates Making up 10382 groups Consisting of 3084 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163395-chr13-+-59725366-59728994 l44 e 94 nr 1000000 chr ENSMUST00000049454-chr7-+-19679893-19683694 l43 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1124345 reads mapping to 407113 Unique genomic coordinates Making up 10738 groups Consisting of 3213 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091813-chr18---78305831-78307295 l44 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 868087 reads mapping to 372328 Unique genomic coordinates Making up 9923 groups Consisting of 2899 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023684-chr16---91635739-91640196 l44 e 96 nr 1000000 chr ENSMUST00000124250-chr9---96992756-96994096 l43 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1040520 reads mapping to 404129 Unique genomic coordinates Making up 10744 groups Consisting of 3176 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000059997-chr2---118579894-118588397 l45 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 832081 reads mapping to 380246 Unique genomic coordinates Making up 10148 groups Consisting of 2978 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000067784-chr14---55254670-55258998 l44 e 98 nr 1000000 chr ENSMUST00000162456-chr8-+-129911910-129913898 l45 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1053158 reads mapping to 385375 Unique genomic coordinates Making up 10079 groups Consisting of 3046 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000066559-chr2-+-132663323-132665899 l45 e 99 nr 1000000 chr ENSMUST00000075941-chr9---101007322-101010799 l45 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1021434 reads mapping to 382926 Unique genomic coordinates Making up 10279 groups Consisting of 2883 clusters