Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 430577 reads mapping to 226967 Unique genomic coordinates Making up 5479 groups Consisting of 517 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000105006-chrX---8539260-8540101 l41 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 514395 reads mapping to 234603 Unique genomic coordinates Making up 5495 groups Consisting of 519 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000064395-chr7-+-56790764-56791902 l43 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 580138 reads mapping to 256569 Unique genomic coordinates Making up 6149 groups Consisting of 571 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 496437 reads mapping to 236857 Unique genomic coordinates Making up 5668 groups Consisting of 581 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000115148-chr9-+-34751455-34752604 l43 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 783686 reads mapping to 254550 Unique genomic coordinates Making up 5968 groups Consisting of 638 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091014-chr3-+-82185316-82186405 l43 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 644511 reads mapping to 246204 Unique genomic coordinates Making up 5963 groups Consisting of 563 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000034304-chr8-+-120257894-120259106 l45 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 545285 reads mapping to 237619 Unique genomic coordinates Making up 5659 groups Consisting of 542 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000103544-chr12---117072161-117072607 l46 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 838247 reads mapping to 244320 Unique genomic coordinates Making up 5837 groups Consisting of 577 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 496360 reads mapping to 238530 Unique genomic coordinates Making up 5676 groups Consisting of 575 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000134240-chr4---42769302-42770109 l43 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 650193 reads mapping to 233306 Unique genomic coordinates Making up 5420 groups Consisting of 525 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 489186 reads mapping to 236584 Unique genomic coordinates Making up 5649 groups Consisting of 510 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 462235 reads mapping to 233386 Unique genomic coordinates Making up 5642 groups Consisting of 511 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 442229 reads mapping to 245865 Unique genomic coordinates Making up 5999 groups Consisting of 577 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125249-chr7-+-4842286-4844213 l41 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 574273 reads mapping to 246728 Unique genomic coordinates Making up 5886 groups Consisting of 576 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 470977 reads mapping to 249773 Unique genomic coordinates Making up 5975 groups Consisting of 595 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000073889-chr7---86593677-86597615 l43 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 562680 reads mapping to 249800 Unique genomic coordinates Making up 5790 groups Consisting of 642 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000068874-chrX---166214310-166216616 l45 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 500302 reads mapping to 237390 Unique genomic coordinates Making up 5723 groups Consisting of 559 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000137488-chr7---148614674-148615317 l45 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 616400 reads mapping to 247293 Unique genomic coordinates Making up 5915 groups Consisting of 515 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000100968-chr6---124141614-124143018 l45 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 593742 reads mapping to 244622 Unique genomic coordinates Making up 5775 groups Consisting of 541 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000151079-chr19-+-6256371-6259619 l42 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 856795 reads mapping to 255729 Unique genomic coordinates Making up 6080 groups Consisting of 611 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 436151 reads mapping to 232683 Unique genomic coordinates Making up 5608 groups Consisting of 518 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 473336 reads mapping to 227275 Unique genomic coordinates Making up 5401 groups Consisting of 504 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 474253 reads mapping to 243008 Unique genomic coordinates Making up 5864 groups Consisting of 583 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000000808-chr8-+-73342724-73345323 l43 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 536289 reads mapping to 242342 Unique genomic coordinates Making up 5782 groups Consisting of 575 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000069741-chr5---35721801-35726024 l43 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 710697 reads mapping to 249740 Unique genomic coordinates Making up 5936 groups Consisting of 561 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000117452-chr7---4777154-4783825 l41 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 577802 reads mapping to 241357 Unique genomic coordinates Making up 5802 groups Consisting of 586 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000123840-chr2---91898876-91899526 l43 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 759437 reads mapping to 254631 Unique genomic coordinates Making up 6046 groups Consisting of 570 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 479282 reads mapping to 231280 Unique genomic coordinates Making up 5548 groups Consisting of 517 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000061755-chrX---35772684-35775528 l43 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 510648 reads mapping to 241889 Unique genomic coordinates Making up 5767 groups Consisting of 591 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 474644 reads mapping to 235820 Unique genomic coordinates Making up 5727 groups Consisting of 515 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 453560 reads mapping to 247003 Unique genomic coordinates Making up 6017 groups Consisting of 548 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000049887-chr5-+-23686399-23689831 l43 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 643121 reads mapping to 247582 Unique genomic coordinates Making up 5900 groups Consisting of 597 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 498197 reads mapping to 239205 Unique genomic coordinates Making up 5769 groups Consisting of 574 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000146835-chrX-+-148613507-148614133 l45 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 501415 reads mapping to 242276 Unique genomic coordinates Making up 5845 groups Consisting of 538 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 486461 reads mapping to 237027 Unique genomic coordinates Making up 5621 groups Consisting of 545 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 481962 reads mapping to 244801 Unique genomic coordinates Making up 5836 groups Consisting of 575 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000070326-chr9-+-83747910-83749036 l43 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 523237 reads mapping to 244090 Unique genomic coordinates Making up 5855 groups Consisting of 552 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 499771 reads mapping to 235048 Unique genomic coordinates Making up 5527 groups Consisting of 516 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000064932-chr6-+-40441237-40442238 l43 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 596851 reads mapping to 231519 Unique genomic coordinates Making up 5579 groups Consisting of 546 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113570-chr9---71014791-71015939 l43 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 516781 reads mapping to 243045 Unique genomic coordinates Making up 5886 groups Consisting of 552 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 440269 reads mapping to 238556 Unique genomic coordinates Making up 5737 groups Consisting of 536 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000155023-chr4---141662227-141663341 l45 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 620357 reads mapping to 254411 Unique genomic coordinates Making up 6056 groups Consisting of 609 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036555-chr9-+-75092277-75093442 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 525432 reads mapping to 236297 Unique genomic coordinates Making up 5514 groups Consisting of 546 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107519-chr7-+-71412346-71414643 l43 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 577739 reads mapping to 248185 Unique genomic coordinates Making up 5959 groups Consisting of 613 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000002292-chr6---71362744-71363844 l43 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 615484 reads mapping to 244639 Unique genomic coordinates Making up 5822 groups Consisting of 585 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 497600 reads mapping to 245184 Unique genomic coordinates Making up 5905 groups Consisting of 583 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 482656 reads mapping to 253124 Unique genomic coordinates Making up 5992 groups Consisting of 576 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166284-chr7---94631831-94633047 l43 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 580536 reads mapping to 233172 Unique genomic coordinates Making up 5508 groups Consisting of 572 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 442745 reads mapping to 234807 Unique genomic coordinates Making up 5658 groups Consisting of 509 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135633-chr7-+-138571443-138572649 l45 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 545257 reads mapping to 247166 Unique genomic coordinates Making up 5863 groups Consisting of 583 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106663-chr7---118697453-118698650 l45 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 598409 reads mapping to 246022 Unique genomic coordinates Making up 5742 groups Consisting of 606 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 467058 reads mapping to 226325 Unique genomic coordinates Making up 5382 groups Consisting of 532 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000123926-chr9---107500005-107507852 l45 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 520474 reads mapping to 252798 Unique genomic coordinates Making up 6069 groups Consisting of 599 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 429247 reads mapping to 245850 Unique genomic coordinates Making up 5871 groups Consisting of 579 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000130067-chr2---9989737-9991854 l41 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 787409 reads mapping to 249203 Unique genomic coordinates Making up 5900 groups Consisting of 558 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144557-chr6---146239008-146240655 l45 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 573690 reads mapping to 235367 Unique genomic coordinates Making up 5604 groups Consisting of 540 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000003313-chr19-+-61167297-61168456 l44 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 872424 reads mapping to 242266 Unique genomic coordinates Making up 5810 groups Consisting of 536 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000105720-chr4---146986046-146988657 l45 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 614658 reads mapping to 251899 Unique genomic coordinates Making up 5956 groups Consisting of 636 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 465098 reads mapping to 234349 Unique genomic coordinates Making up 5586 groups Consisting of 544 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 434751 reads mapping to 232807 Unique genomic coordinates Making up 5611 groups Consisting of 521 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113358-chrX-+-117403868-117404760 l45 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 506487 reads mapping to 235697 Unique genomic coordinates Making up 5541 groups Consisting of 543 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 494730 reads mapping to 240795 Unique genomic coordinates Making up 5716 groups Consisting of 529 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035077-chr9-+-110933021-110934162 l45 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 532064 reads mapping to 248393 Unique genomic coordinates Making up 5892 groups Consisting of 558 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 453476 reads mapping to 236679 Unique genomic coordinates Making up 5670 groups Consisting of 551 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098860-chr8---26859699-26861764 l43 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 547817 reads mapping to 247283 Unique genomic coordinates Making up 5904 groups Consisting of 576 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000047207-chr4---153413111-153414265 l45 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 694485 reads mapping to 238890 Unique genomic coordinates Making up 5595 groups Consisting of 568 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 402603 reads mapping to 216224 Unique genomic coordinates Making up 5162 groups Consisting of 514 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000084450-chr9---88752070-88753667 l43 e 67 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 522236 reads mapping to 237413 Unique genomic coordinates Making up 5672 groups Consisting of 565 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166168-chr9---60518602-60519668 l43 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 524571 reads mapping to 248732 Unique genomic coordinates Making up 5933 groups Consisting of 577 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173179-chr7-+-92237278-92239669 l43 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 751346 reads mapping to 235405 Unique genomic coordinates Making up 5574 groups Consisting of 574 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 487028 reads mapping to 233255 Unique genomic coordinates Making up 5567 groups Consisting of 550 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000149260-chrX-+-143421026-143423871 l45 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 514920 reads mapping to 236678 Unique genomic coordinates Making up 5727 groups Consisting of 538 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098346-chr7---87511255-87516072 l43 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 551880 reads mapping to 246292 Unique genomic coordinates Making up 5937 groups Consisting of 550 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 496611 reads mapping to 236041 Unique genomic coordinates Making up 5682 groups Consisting of 531 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121226-chr17---24487413-24487974 l44 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 867767 reads mapping to 243177 Unique genomic coordinates Making up 5865 groups Consisting of 551 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000116947-chr4-+-126054383-126054475 l45 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 648303 reads mapping to 248952 Unique genomic coordinates Making up 5966 groups Consisting of 609 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 492603 reads mapping to 232712 Unique genomic coordinates Making up 5458 groups Consisting of 543 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000032728-chr7-+-72835557-72836977 l43 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 575055 reads mapping to 242553 Unique genomic coordinates Making up 5829 groups Consisting of 562 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000043616-chr4---107922600-107923978 l45 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 614925 reads mapping to 257708 Unique genomic coordinates Making up 6228 groups Consisting of 581 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 440747 reads mapping to 237381 Unique genomic coordinates Making up 5713 groups Consisting of 550 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000145049-chr7-+-59135701-59136380 l43 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 544880 reads mapping to 244304 Unique genomic coordinates Making up 5869 groups Consisting of 580 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000141824-chr5-+-36277701-36279281 l43 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 600066 reads mapping to 232054 Unique genomic coordinates Making up 5572 groups Consisting of 539 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000164693-chrX---93551974-93553082 l43 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 515220 reads mapping to 242634 Unique genomic coordinates Making up 5859 groups Consisting of 559 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000068767-chr7-+-27248613-27249783 l43 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 582821 reads mapping to 250418 Unique genomic coordinates Making up 5962 groups Consisting of 610 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026743-chr9-+-108845589-108847984 l45 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 511555 reads mapping to 232645 Unique genomic coordinates Making up 5451 groups Consisting of 535 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167794-chr1---80267599-80268785 l43 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 965285 reads mapping to 243143 Unique genomic coordinates Making up 5756 groups Consisting of 544 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000141203-chr5---124753683-124754786 l45 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 686293 reads mapping to 242894 Unique genomic coordinates Making up 5727 groups Consisting of 559 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000031108-chr5-+-66361555-66363087 l43 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 601532 reads mapping to 247914 Unique genomic coordinates Making up 6034 groups Consisting of 559 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 489727 reads mapping to 240262 Unique genomic coordinates Making up 5753 groups Consisting of 599 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 479647 reads mapping to 228080 Unique genomic coordinates Making up 5561 groups Consisting of 526 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000134245-chr7---127816953-127819290 l45 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 642854 reads mapping to 240720 Unique genomic coordinates Making up 5782 groups Consisting of 585 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000086280-chr9---22057799-22058891 l43 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 533361 reads mapping to 251892 Unique genomic coordinates Making up 5977 groups Consisting of 587 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000069009-chr8---118216532-118217592 l45 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 534559 reads mapping to 240247 Unique genomic coordinates Making up 5774 groups Consisting of 554 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000130412-chr8-+-47065169-47066493 l43 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 541561 reads mapping to 248123 Unique genomic coordinates Making up 5968 groups Consisting of 590 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 475547 reads mapping to 253076 Unique genomic coordinates Making up 6038 groups Consisting of 606 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 463465 reads mapping to 231156 Unique genomic coordinates Making up 5484 groups Consisting of 520 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000057972-chr9-+-67736993-67738696 l43 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 518227 reads mapping to 252746 Unique genomic coordinates Making up 6024 groups Consisting of 609 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173833-chr8---25757758-25758897 l43 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 536871 reads mapping to 243346 Unique genomic coordinates Making up 5744 groups Consisting of 611 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000126339-chrX---135801114-135802198 l45 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 503691 reads mapping to 244733 Unique genomic coordinates Making up 5924 groups Consisting of 563 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000078908-chr7-+-20106783-20110399 l43 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 573657 reads mapping to 241849 Unique genomic coordinates Making up 5872 groups Consisting of 547 clusters