Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000153463-chr14-+-35577378-35579200 l44 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 949741 reads mapping to 318373 Unique genomic coordinates Making up 8269 groups Consisting of 2390 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099075-chr3-+-65487314-65490101 l43 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 800112 reads mapping to 324363 Unique genomic coordinates Making up 8517 groups Consisting of 2441 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000084949-chr4---4704840-4706002 l41 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 806577 reads mapping to 361355 Unique genomic coordinates Making up 9367 groups Consisting of 2727 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167998-chr3-+-89008869-89012603 l43 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 733959 reads mapping to 330764 Unique genomic coordinates Making up 8718 groups Consisting of 2606 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000090559-chr2---92251283-92254604 l43 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 873373 reads mapping to 348728 Unique genomic coordinates Making up 8954 groups Consisting of 2668 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000057394-chr17---38441464-38442405 l44 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 940600 reads mapping to 350771 Unique genomic coordinates Making up 9068 groups Consisting of 2563 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000046288-chr17-+-31657060-31657706 l44 e 6 nr 1000000 chr ENSMUST00000046288-chr17-+-31657060-31657706 l44 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1386905 reads mapping to 334316 Unique genomic coordinates Making up 8710 groups Consisting of 2562 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023813-chr15-+-102350406-102354107 l46 e 7 nr 1000000 chr ENSMUST00000172906-chr8---125413039-125421107 l45 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1061361 reads mapping to 342192 Unique genomic coordinates Making up 8916 groups Consisting of 2590 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000097896-chr4-+-123539253-123540408 l45 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 821018 reads mapping to 329200 Unique genomic coordinates Making up 8570 groups Consisting of 2411 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029909-chr4-+-21837066-21839309 l43 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 725635 reads mapping to 323252 Unique genomic coordinates Making up 8384 groups Consisting of 2493 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022433-chr14-+-27625255-27626510 l44 e 10 nr 1000000 chr ENSMUST00000041370-chrX---159224049-159226110 l45 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1001818 reads mapping to 330250 Unique genomic coordinates Making up 8513 groups Consisting of 2556 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000041618-chr2---179646851-179648811 l45 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 779345 reads mapping to 325261 Unique genomic coordinates Making up 8493 groups Consisting of 2447 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025973-chr19---40398737-40402612 l44 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 840297 reads mapping to 345968 Unique genomic coordinates Making up 8971 groups Consisting of 2551 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159574-chr13-+-104918809-104919913 l46 e 13 nr 1000000 chr ENSMUST00000159574-chr13-+-104918809-104919913 l46 e 13 nr 1500000 chr ENSMUST00000138966-chr4---112739551-112740613 l45 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1729554 reads mapping to 346640 Unique genomic coordinates Making up 9026 groups Consisting of 2596 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000063988-chr3-+-22101519-22103414 l43 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 792999 reads mapping to 348628 Unique genomic coordinates Making up 9021 groups Consisting of 2617 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107195-chr3---95053228-95055115 l43 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 795718 reads mapping to 344297 Unique genomic coordinates Making up 8986 groups Consisting of 2566 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025581-chr19-+-11628794-11629916 l44 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 813441 reads mapping to 332505 Unique genomic coordinates Making up 8611 groups Consisting of 2571 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029663-chr3---132329849-132331017 l45 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 840390 reads mapping to 352624 Unique genomic coordinates Making up 9170 groups Consisting of 2768 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000164768-chr11-+-102724651-102728718 l46 e 18 nr 1000000 chr ENSMUST00000153277-chr7---134848502-134850818 l45 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1183941 reads mapping to 340105 Unique genomic coordinates Making up 8851 groups Consisting of 2564 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025468-chr18-+-61423077-61425219 l44 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 928951 reads mapping to 359832 Unique genomic coordinates Making up 9286 groups Consisting of 2663 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000044684-chr5---101195207-101196320 l45 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 651188 reads mapping to 324334 Unique genomic coordinates Making up 8427 groups Consisting of 2519 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000147611-chr4---91039083-91039721 l43 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 683447 reads mapping to 320377 Unique genomic coordinates Making up 8367 groups Consisting of 2378 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000139000-chr2---24690622-24692522 l43 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 811772 reads mapping to 337669 Unique genomic coordinates Making up 8820 groups Consisting of 2558 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000068586-chr2---92205203-92208523 l43 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 911599 reads mapping to 341104 Unique genomic coordinates Making up 8874 groups Consisting of 2549 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136537-chr2---64986366-64989724 l43 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 773569 reads mapping to 349930 Unique genomic coordinates Making up 9156 groups Consisting of 2673 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000068264-chr11---18780433-18782425 l44 e 25 nr 1000000 chr ENSMUST00000113528-chr19-+-6221173-6224225 l42 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1382437 reads mapping to 336516 Unique genomic coordinates Making up 8694 groups Consisting of 2463 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000096494-chr15---7172248-7173326 l42 e 26 nr 1000000 chr ENSMUST00000061468-chr7---134848492-134849826 l45 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1118752 reads mapping to 354586 Unique genomic coordinates Making up 9288 groups Consisting of 2761 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125881-chr14-+-26514459-26518327 l44 e 27 nr 1000000 chr ENSMUST00000121564-chr9---35030699-35031827 l43 e 27 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1143197 reads mapping to 326932 Unique genomic coordinates Making up 8445 groups Consisting of 2435 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000145668-chr4-+-132254445-132255528 l45 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 839289 reads mapping to 332330 Unique genomic coordinates Making up 8718 groups Consisting of 2452 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029240-chr3-+-28617091-28618929 l43 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 810243 reads mapping to 326227 Unique genomic coordinates Making up 8618 groups Consisting of 2452 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022369-chr14-+-21786260-21787330 l44 e 30 nr 1000000 chr ENSMUST00000132333-chrX-+-82334656-82335730 l43 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1015361 reads mapping to 349689 Unique genomic coordinates Making up 9138 groups Consisting of 2655 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166157-chr3---126719234-126720431 l45 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 744408 reads mapping to 347476 Unique genomic coordinates Making up 9098 groups Consisting of 2693 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000019913-chr10-+-34327112-34331032 l44 e 32 nr 1000000 chr ENSMUST00000127716-chr18---64329530-64330632 l44 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1337290 reads mapping to 341487 Unique genomic coordinates Making up 8775 groups Consisting of 2564 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138372-chr2---117242828-117243433 l45 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 767669 reads mapping to 339759 Unique genomic coordinates Making up 8837 groups Consisting of 2541 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000100733-chr15---27775965-27777734 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 1110741 reads mapping to 330278 Unique genomic coordinates Making up 8588 groups Consisting of 2526 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000146711-chr17-+-35370605-35371335 l44 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 897040 reads mapping to 351594 Unique genomic coordinates Making up 9099 groups Consisting of 2682 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022340-chr14-+-20624020-20625736 l44 e 36 nr 1000000 chr ENSMUST00000125615-chr9-+-77960626-77961236 l43 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1030230 reads mapping to 335757 Unique genomic coordinates Making up 8717 groups Consisting of 2498 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000043551-chr5---3701305-3703537 l41 e 37 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 730918 reads mapping to 324067 Unique genomic coordinates Making up 8449 groups Consisting of 2489 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114787-chr16---37115028-37116638 l44 e 38 nr 1000000 chr ENSMUST00000069718-chr8-+-94189681-94192338 l43 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1049095 reads mapping to 321589 Unique genomic coordinates Making up 8332 groups Consisting of 2424 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091288-chr2-+-131735664-131736239 l45 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 846990 reads mapping to 345831 Unique genomic coordinates Making up 8982 groups Consisting of 2624 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000172860-chr3-+-19886859-19889740 l43 e 40 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 822170 reads mapping to 339027 Unique genomic coordinates Making up 8960 groups Consisting of 2551 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039205-chr17-+-80582032-80584441 l44 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 986619 reads mapping to 358040 Unique genomic coordinates Making up 9295 groups Consisting of 2557 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161956-chr3-+-65157689-65162742 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 990458 reads mapping to 330717 Unique genomic coordinates Making up 8554 groups Consisting of 2496 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000172105-chr4---126093972-126095143 l45 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 697550 reads mapping to 341875 Unique genomic coordinates Making up 9004 groups Consisting of 2673 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029024-chr2-+-173526023-173532844 l45 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 958147 reads mapping to 333627 Unique genomic coordinates Making up 8754 groups Consisting of 2557 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000017348-chr11-+-98526870-98528445 l44 e 45 nr 1000000 chr ENSMUST00000117157-chr4-+-143503760-143506345 l45 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1211801 reads mapping to 347568 Unique genomic coordinates Making up 9083 groups Consisting of 2606 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030014-chr4-+-46157157-46158846 l43 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 733953 reads mapping to 352068 Unique genomic coordinates Making up 9242 groups Consisting of 2683 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113516-chr5---76344276-76346747 l43 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 640377 reads mapping to 324132 Unique genomic coordinates Making up 8679 groups Consisting of 2441 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000162427-chr5---21550282-21551348 l43 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 780468 reads mapping to 332807 Unique genomic coordinates Making up 8605 groups Consisting of 2531 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000053570-chr11-+-11387174-11389149 l44 e 49 nr 1000000 chr ENSMUST00000030257-chr4-+-100537087-100538149 l45 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1209752 reads mapping to 344244 Unique genomic coordinates Making up 8812 groups Consisting of 2552 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000055930-chr2-+-68553693-68555850 l43 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 974188 reads mapping to 342746 Unique genomic coordinates Making up 8882 groups Consisting of 2610 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000126125-chr5-+-103092602-103096851 l45 e 51 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 716300 reads mapping to 317512 Unique genomic coordinates Making up 8286 groups Consisting of 2408 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000093971-chr3---132553228-132554952 l45 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 869584 reads mapping to 348651 Unique genomic coordinates Making up 9095 groups Consisting of 2592 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107508-chr11-+-98490161-98491753 l44 e 53 nr 1000000 chr ENSMUST00000054050-chr6-+-48626128-48626753 l43 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1250887 reads mapping to 344960 Unique genomic coordinates Making up 9008 groups Consisting of 2638 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107272-chr3---94576550-94579454 l43 e 54 nr 1000000 chr ENSMUST00000121227-chr9---79546556-79548854 l43 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1043003 reads mapping to 344872 Unique genomic coordinates Making up 9107 groups Consisting of 2651 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000171739-chr3---81767344-81768455 l43 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 749156 reads mapping to 330160 Unique genomic coordinates Making up 8646 groups Consisting of 2473 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142292-chr4-+-94718225-94718956 l43 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 709150 reads mapping to 339626 Unique genomic coordinates Making up 8873 groups Consisting of 2633 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000128535-chr2-+-127425248-127428757 l45 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 745162 reads mapping to 347776 Unique genomic coordinates Making up 9164 groups Consisting of 2655 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109822-chr11---5800823-5803758 l42 e 58 nr 1000000 chr ENSMUST00000124183-chr2---24537996-24539058 l43 e 58 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1335756 reads mapping to 327300 Unique genomic coordinates Making up 8540 groups Consisting of 2471 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000162461-chr6-+-119860566-119861659 l45 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 642239 reads mapping to 324316 Unique genomic coordinates Making up 8554 groups Consisting of 2461 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000061856-chr19---55146702-55147760 l44 e 60 nr 1000000 chr ENSMUST00000098986-chr9-+-8957830-8958960 l41 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1057104 reads mapping to 330702 Unique genomic coordinates Making up 8612 groups Consisting of 2534 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030676-chr4-+-125362738-125363961 l45 e 61 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 804669 reads mapping to 333537 Unique genomic coordinates Making up 8674 groups Consisting of 2537 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025228-chr18---34802953-34805262 l44 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 928633 reads mapping to 349076 Unique genomic coordinates Making up 8921 groups Consisting of 2626 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030622-chr4-+-134489871-134493463 l45 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 683096 reads mapping to 331818 Unique genomic coordinates Making up 8673 groups Consisting of 2540 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000134720-chr2---76759108-76760164 l43 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 803529 reads mapping to 348240 Unique genomic coordinates Making up 9121 groups Consisting of 2575 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000174259-chr14-+-56197197-56200365 l44 e 65 nr 1000000 chr ENSMUST00000135695-chr9---111157632-111161565 l45 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1031244 reads mapping to 329256 Unique genomic coordinates Making up 8717 groups Consisting of 2492 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000094018-chr7-+-136464503-136465566 l45 e 66 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 588244 reads mapping to 299615 Unique genomic coordinates Making up 7719 groups Consisting of 2234 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109523-chr2-+-157740389-157741167 l45 e 67 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 839451 reads mapping to 332825 Unique genomic coordinates Making up 8719 groups Consisting of 2594 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107727-chr3-+-82183500-82184668 l43 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 835163 reads mapping to 353979 Unique genomic coordinates Making up 9215 groups Consisting of 2692 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110325-chr2-+-128655746-128657869 l45 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 935685 reads mapping to 330237 Unique genomic coordinates Making up 8564 groups Consisting of 2482 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099930-chr2---85002491-85004170 l43 e 70 nr 1000000 chr ENSMUST00000113320-chrX-+-126994907-127000370 l45 e 70 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1005326 reads mapping to 324834 Unique genomic coordinates Making up 8399 groups Consisting of 2411 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029999-chr4-+-45036851-45041471 l43 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 715383 reads mapping to 329063 Unique genomic coordinates Making up 8652 groups Consisting of 2514 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000154246-chr2---27738445-27742572 l43 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 849531 reads mapping to 348271 Unique genomic coordinates Making up 9098 groups Consisting of 2630 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000143276-chr5-+-114688127-114691173 l45 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 801222 reads mapping to 325829 Unique genomic coordinates Making up 8519 groups Consisting of 2442 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028135-chr2-+-32775973-32780774 l43 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 853812 reads mapping to 345025 Unique genomic coordinates Making up 8900 groups Consisting of 2557 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000129308-chr3---89209003-89210375 l43 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 891771 reads mapping to 342269 Unique genomic coordinates Making up 8926 groups Consisting of 2669 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000002502-chr3-+-20015958-20018376 l43 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 844186 reads mapping to 323688 Unique genomic coordinates Making up 8401 groups Consisting of 2426 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000070607-chr4---86224759-86230277 l43 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 746613 reads mapping to 335500 Unique genomic coordinates Making up 8729 groups Consisting of 2532 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136669-chr4---94252451-94254778 l43 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 932834 reads mapping to 356758 Unique genomic coordinates Making up 9278 groups Consisting of 2630 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023559-chr16---21773068-21774179 l44 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 890446 reads mapping to 333107 Unique genomic coordinates Making up 8635 groups Consisting of 2517 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000084301-chr4---123147750-123154080 l45 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 700756 reads mapping to 339457 Unique genomic coordinates Making up 8999 groups Consisting of 2601 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035471-chr17-+-68112611-68114681 l44 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 874746 reads mapping to 323331 Unique genomic coordinates Making up 8472 groups Consisting of 2452 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000124711-chr5---37203686-37207982 l43 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 712758 reads mapping to 341792 Unique genomic coordinates Making up 8901 groups Consisting of 2558 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135024-chr4---82150135-82151683 l43 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 779617 reads mapping to 353775 Unique genomic coordinates Making up 9193 groups Consisting of 2677 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000154982-chr17---24247315-24248584 l44 e 84 nr 1000000 chr ENSMUST00000036019-chr5-+-97140896-97142084 l43 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1175991 reads mapping to 323934 Unique genomic coordinates Making up 8406 groups Consisting of 2451 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000090929-chr3---88890195-88897285 l43 e 85 nr 1000000 chr ENSMUST00000080654-chr7---148461387-148462685 l45 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1095472 reads mapping to 343977 Unique genomic coordinates Making up 9037 groups Consisting of 2560 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110321-chr12-+-83441149-83443986 l44 e 86 nr 1000000 chr ENSMUST00000041015-chr7-+-63423696-63424886 l43 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1077633 reads mapping to 336717 Unique genomic coordinates Making up 8718 groups Consisting of 2569 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000060642-chr15-+-91529814-91531587 l44 e 87 nr 1000000 chr ENSMUST00000126595-chr5-+-32582972-32584687 l43 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1222142 reads mapping to 346499 Unique genomic coordinates Making up 8904 groups Consisting of 2632 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000089677-chr16-+-33420907-33421988 l44 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 986156 reads mapping to 334690 Unique genomic coordinates Making up 8666 groups Consisting of 2514 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029907-chr4-+-6128939-6130089 l41 e 89 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 716175 reads mapping to 321259 Unique genomic coordinates Making up 8407 groups Consisting of 2391 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114076-chr16---91068777-91069390 l44 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 889814 reads mapping to 327509 Unique genomic coordinates Making up 8617 groups Consisting of 2461 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106623-chr11-+-113514718-113521191 l46 e 91 nr 1000000 chr ENSMUST00000149002-chr4-+-140873897-140875491 l45 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1182688 reads mapping to 356547 Unique genomic coordinates Making up 9312 groups Consisting of 2620 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000063886-chr2-+-48747149-48748292 l43 e 92 nr 1000000 chr ENSMUST00000094665-chr2---120100470-120101692 l45 e 92 nr 1500000 chr ENSMUST00000094665-chr2---120100470-120101692 l45 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1834120 reads mapping to 341044 Unique genomic coordinates Making up 8822 groups Consisting of 2589 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000139555-chr4-+-151347089-151350793 l45 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 764242 reads mapping to 342790 Unique genomic coordinates Making up 8996 groups Consisting of 2623 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036439-chr15---13102769-13103394 l44 e 94 nr 1000000 chr ENSMUST00000112930-chrX-+-138024153-138025194 l45 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1003715 reads mapping to 360622 Unique genomic coordinates Making up 9368 groups Consisting of 2722 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000045196-chr2---163993048-163995495 l45 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 766388 reads mapping to 329623 Unique genomic coordinates Making up 8588 groups Consisting of 2495 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114033-chr17-+-35047136-35050996 l44 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 926372 reads mapping to 358041 Unique genomic coordinates Making up 9327 groups Consisting of 2683 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030014-chr4-+-46164388-46166497 l43 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 735631 reads mapping to 336742 Unique genomic coordinates Making up 8817 groups Consisting of 2530 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000060188-chr16---31264891-31265998 l44 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 932491 reads mapping to 341226 Unique genomic coordinates Making up 8783 groups Consisting of 2591 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107664-chr3-+-85920241-85921299 l43 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 905365 reads mapping to 339379 Unique genomic coordinates Making up 8970 groups Consisting of 2505 clusters