Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159778-chr17---90960200-90960700 l44 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 870571 reads mapping to 349565 Unique genomic coordinates Making up 9545 groups Consisting of 3414 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000072602-chr5-+-122660401-122660901 l45 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 624065 reads mapping to 343894 Unique genomic coordinates Making up 9561 groups Consisting of 3450 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102679-chr2---73282002-73282502 l43 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 784324 reads mapping to 372322 Unique genomic coordinates Making up 10024 groups Consisting of 3611 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136843-chr4---129271803-129272303 l45 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 702183 reads mapping to 347257 Unique genomic coordinates Making up 9435 groups Consisting of 3386 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144504-chr4---133789842-133790404 l45 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 761110 reads mapping to 363940 Unique genomic coordinates Making up 10053 groups Consisting of 3669 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144637-chr4---99336605-99337105 l43 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 693704 reads mapping to 364510 Unique genomic coordinates Making up 10049 groups Consisting of 3543 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028728-chr2---120775906-120776406 l45 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 823150 reads mapping to 356908 Unique genomic coordinates Making up 9691 groups Consisting of 3440 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169132-chr5-+-31218807-31219307 l43 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 679263 reads mapping to 356635 Unique genomic coordinates Making up 9743 groups Consisting of 3459 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000050933-chr4---143749585-143750108 l45 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 767712 reads mapping to 367266 Unique genomic coordinates Making up 9876 groups Consisting of 3671 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000037141-chr3---51325409-51325909 l43 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 778119 reads mapping to 360174 Unique genomic coordinates Making up 10035 groups Consisting of 3484 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022609-chr14---66184310-66184810 l44 e 10 nr 1000000 chr ENSMUST00000093812-chr9-+-78552910-78553410 l43 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1040520 reads mapping to 373413 Unique genomic coordinates Making up 10219 groups Consisting of 3841 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110709-chr5-+-144689135-144689811 l45 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 693228 reads mapping to 359501 Unique genomic coordinates Making up 9906 groups Consisting of 3606 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000145549-chr2---180116312-180116812 l45 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 813482 reads mapping to 379585 Unique genomic coordinates Making up 10327 groups Consisting of 3789 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000031038-chr5-+-73701013-73701513 l43 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 677995 reads mapping to 360528 Unique genomic coordinates Making up 9933 groups Consisting of 3567 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114349-chr2---25105046-25105314 l43 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 916232 reads mapping to 363010 Unique genomic coordinates Making up 9896 groups Consisting of 3556 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000134408-chr2---126668715-126669215 l45 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 813171 reads mapping to 351529 Unique genomic coordinates Making up 9492 groups Consisting of 3452 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159159-chr3-+-137949916-137950416 l45 e 16 nr 1000000 chr ENSMUST00000125589-chr5-+-32033416-32033916 l43 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1234344 reads mapping to 363867 Unique genomic coordinates Making up 9866 groups Consisting of 3599 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000058030-chr4-+-88802517-88803017 l43 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 713779 reads mapping to 355925 Unique genomic coordinates Making up 9813 groups Consisting of 3640 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148578-chr3---98546618-98547118 l43 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 994648 reads mapping to 357118 Unique genomic coordinates Making up 9705 groups Consisting of 3512 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000152297-chr4-+-154961893-154962719 l45 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 707531 reads mapping to 367858 Unique genomic coordinates Making up 10045 groups Consisting of 3586 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029840-chr3-+-146118120-146118620 l45 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 714140 reads mapping to 352138 Unique genomic coordinates Making up 9685 groups Consisting of 3523 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029770-chr3---121474721-121475221 l45 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 724773 reads mapping to 349522 Unique genomic coordinates Making up 9467 groups Consisting of 3429 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000059155-chr5-+-28400211-28401022 l43 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 693720 reads mapping to 362742 Unique genomic coordinates Making up 9861 groups Consisting of 3585 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000126465-chr4-+-57721823-57722323 l43 e 23 nr 1000000 chr ENSMUST00000075578-chr8---126478475-126478623 l45 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1216739 reads mapping to 369041 Unique genomic coordinates Making up 10026 groups Consisting of 3658 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000040465-chr3---144753824-144754324 l45 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 792958 reads mapping to 368632 Unique genomic coordinates Making up 10028 groups Consisting of 3657 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000112055-chr2---73041525-73042025 l43 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 814336 reads mapping to 372565 Unique genomic coordinates Making up 10192 groups Consisting of 3685 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000090750-chr3---97555926-97556426 l43 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 799626 reads mapping to 359719 Unique genomic coordinates Making up 9873 groups Consisting of 3543 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098013-chr4---70037327-70037827 l43 e 27 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 753181 reads mapping to 368223 Unique genomic coordinates Making up 9886 groups Consisting of 3679 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000134720-chr2---76679893-76680828 l43 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 787270 reads mapping to 367874 Unique genomic coordinates Making up 9908 groups Consisting of 3552 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000129602-chr4---141153529-141154029 l45 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 705922 reads mapping to 359508 Unique genomic coordinates Making up 9710 groups Consisting of 3596 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099092-chr2-+-164819611-164820430 l45 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 920404 reads mapping to 369631 Unique genomic coordinates Making up 10150 groups Consisting of 3694 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028233-chr2---34894231-34894731 l43 e 31 nr 1000000 chr ENSMUST00000117782-chr3---95486269-95487231 l43 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1482188 reads mapping to 366908 Unique genomic coordinates Making up 10007 groups Consisting of 3600 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000076335-chr2-+-124479994-124480532 l45 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 830140 reads mapping to 365581 Unique genomic coordinates Making up 10009 groups Consisting of 3608 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169021-chr2-+-156119314-156119833 l45 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 752644 reads mapping to 351720 Unique genomic coordinates Making up 9601 groups Consisting of 3452 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000164573-chr3---120859434-120859934 l45 e 34 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 735892 reads mapping to 362680 Unique genomic coordinates Making up 9871 groups Consisting of 3661 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039608-chr18-+-75212135-75212635 l44 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 833960 reads mapping to 356561 Unique genomic coordinates Making up 9700 groups Consisting of 3500 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000128463-chr4-+-43903336-43903836 l43 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 718442 reads mapping to 354798 Unique genomic coordinates Making up 9811 groups Consisting of 3481 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133741-chr17---45816663-45817537 l44 e 37 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 901854 reads mapping to 363881 Unique genomic coordinates Making up 9863 groups Consisting of 3645 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121884-chr4---114811338-114811838 l45 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 708471 reads mapping to 357467 Unique genomic coordinates Making up 9698 groups Consisting of 3531 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110501-chr2---124913439-124913939 l45 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 840211 reads mapping to 369608 Unique genomic coordinates Making up 10094 groups Consisting of 3633 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133499-chr4-+-124248540-124249040 l45 e 40 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 678703 reads mapping to 359178 Unique genomic coordinates Making up 9940 groups Consisting of 3559 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000105788-chr4---140964560-140965241 l45 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 692024 reads mapping to 369202 Unique genomic coordinates Making up 10127 groups Consisting of 3687 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000117486-chr2---27933901-27934642 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 801613 reads mapping to 359159 Unique genomic coordinates Making up 9846 groups Consisting of 3598 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106708-chr4---107702043-107702543 l45 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 705445 reads mapping to 369469 Unique genomic coordinates Making up 9947 groups Consisting of 3589 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113555-chr2---30908600-30909544 l43 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 846603 reads mapping to 362033 Unique genomic coordinates Making up 9831 groups Consisting of 3604 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106916-chr4---101640845-101641345 l45 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 718002 reads mapping to 362924 Unique genomic coordinates Making up 10097 groups Consisting of 3613 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107154-chr3-+-95366546-95367046 l43 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 829769 reads mapping to 363929 Unique genomic coordinates Making up 10114 groups Consisting of 3725 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000069293-chr1-+-46142547-46143047 l43 e 47 nr 1000000 chr ENSMUST00000138820-chr5---38604047-38604547 l43 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1173641 reads mapping to 361801 Unique genomic coordinates Making up 9843 groups Consisting of 3498 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000156558-chr4---136231448-136231948 l45 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 681104 reads mapping to 363536 Unique genomic coordinates Making up 9871 groups Consisting of 3587 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000094376-chr11---20609749-20610249 l44 e 49 nr 1000000 chr ENSMUST00000075836-chr4---98659149-98659649 l43 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1211613 reads mapping to 363470 Unique genomic coordinates Making up 9900 groups Consisting of 3540 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136286-chr19---37163050-37163550 l44 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 820464 reads mapping to 359990 Unique genomic coordinates Making up 9835 groups Consisting of 3575 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138966-chr4---112739551-112740051 l45 e 51 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 690289 reads mapping to 350307 Unique genomic coordinates Making up 9645 groups Consisting of 3511 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098538-chr3-+-144798698-144799552 l45 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 716860 reads mapping to 376176 Unique genomic coordinates Making up 10343 groups Consisting of 3884 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165709-chr4-+-106062953-106063453 l45 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 722656 reads mapping to 360613 Unique genomic coordinates Making up 9918 groups Consisting of 3611 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000037409-chr3-+-100734854-100735354 l45 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 709682 reads mapping to 370480 Unique genomic coordinates Making up 10061 groups Consisting of 3758 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029836-chr3---146249355-146249855 l45 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 736927 reads mapping to 370594 Unique genomic coordinates Making up 10082 groups Consisting of 3671 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170552-chr3-+-54519178-54519456 l43 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 785551 reads mapping to 378146 Unique genomic coordinates Making up 10214 groups Consisting of 3679 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000014499-chr2---128452357-128452857 l45 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 898945 reads mapping to 353352 Unique genomic coordinates Making up 9537 groups Consisting of 3574 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000055131-chr4-+-137160558-137161058 l45 e 58 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 713965 reads mapping to 362476 Unique genomic coordinates Making up 9892 groups Consisting of 3542 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000043812-chr3---142457459-142457959 l45 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 770976 reads mapping to 360249 Unique genomic coordinates Making up 9754 groups Consisting of 3527 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028909-chr2---144087760-144088260 l45 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 793411 reads mapping to 358065 Unique genomic coordinates Making up 9846 groups Consisting of 3537 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029461-chr3-+-99841961-99842461 l43 e 61 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 772901 reads mapping to 372766 Unique genomic coordinates Making up 9893 groups Consisting of 3683 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000062145-chr4-+-62203817-62204162 l43 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 725186 reads mapping to 364620 Unique genomic coordinates Making up 9980 groups Consisting of 3558 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106707-chr3---107429774-107429863 l45 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 928288 reads mapping to 363780 Unique genomic coordinates Making up 9944 groups Consisting of 3566 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000137293-chr4-+-21751064-21751564 l43 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 762982 reads mapping to 366168 Unique genomic coordinates Making up 9855 groups Consisting of 3559 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136812-chr4-+-135810485-135811065 l45 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 668806 reads mapping to 355044 Unique genomic coordinates Making up 9779 groups Consisting of 3557 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030420-chr4---136490503-136490966 l45 e 66 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 658324 reads mapping to 347593 Unique genomic coordinates Making up 9450 groups Consisting of 3368 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000150189-chr2-+-136328767-136329267 l45 e 67 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 850690 reads mapping to 356710 Unique genomic coordinates Making up 9728 groups Consisting of 3522 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107155-chr4---86674268-86674768 l43 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 710483 reads mapping to 370117 Unique genomic coordinates Making up 10107 groups Consisting of 3614 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000124788-chr2-+-144292169-144292669 l45 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 728699 reads mapping to 350768 Unique genomic coordinates Making up 9740 groups Consisting of 3470 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135299-chr4-+-132222570-132223070 l45 e 70 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 710427 reads mapping to 351013 Unique genomic coordinates Making up 9493 groups Consisting of 3371 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173827-chr3-+-29920971-29921471 l43 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 744985 reads mapping to 353468 Unique genomic coordinates Making up 9719 groups Consisting of 3497 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161577-chr3---132664972-132665472 l45 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 841547 reads mapping to 347045 Unique genomic coordinates Making up 9585 groups Consisting of 3508 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167733-chr4-+-133704773-133705273 l45 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 681485 reads mapping to 359272 Unique genomic coordinates Making up 9880 groups Consisting of 3490 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091818-chr2---112501274-112501774 l45 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 887733 reads mapping to 370550 Unique genomic coordinates Making up 10082 groups Consisting of 3676 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109266-chr2---165632675-165633175 l45 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 790597 reads mapping to 355662 Unique genomic coordinates Making up 9684 groups Consisting of 3523 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000147343-chr5---116470476-116470976 l45 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 692163 reads mapping to 351783 Unique genomic coordinates Making up 9544 groups Consisting of 3489 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000042221-chr4---14446677-14447177 l43 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 729183 reads mapping to 364495 Unique genomic coordinates Making up 9907 groups Consisting of 3651 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163105-chr3---135897078-135897578 l45 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 792665 reads mapping to 379185 Unique genomic coordinates Making up 10413 groups Consisting of 3744 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110168-chr15---57883279-57883779 l44 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 894495 reads mapping to 360817 Unique genomic coordinates Making up 10034 groups Consisting of 3606 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000092730-chr4-+-100219280-100219780 l45 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 684247 reads mapping to 354015 Unique genomic coordinates Making up 9742 groups Consisting of 3543 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000048430-chr4---82529981-82530481 l43 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 731740 reads mapping to 356165 Unique genomic coordinates Making up 9609 groups Consisting of 3454 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025338-chr17-+-37201682-37202182 l44 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 854783 reads mapping to 358214 Unique genomic coordinates Making up 9753 groups Consisting of 3492 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170156-chr13---11944883-11945383 l44 e 83 nr 1000000 chr ENSMUST00000041860-chr7-+-105131483-105131983 l45 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1099295 reads mapping to 366771 Unique genomic coordinates Making up 9973 groups Consisting of 3613 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000155749-chr4-+-101119884-101120384 l45 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 773347 reads mapping to 358595 Unique genomic coordinates Making up 9922 groups Consisting of 3491 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000124780-chr5-+-33329085-33329585 l43 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 669548 reads mapping to 352727 Unique genomic coordinates Making up 9750 groups Consisting of 3491 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161851-chr3-+-65531178-65532086 l43 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 971716 reads mapping to 373565 Unique genomic coordinates Making up 10251 groups Consisting of 3671 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028814-chr2---131854987-131855487 l45 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 751433 reads mapping to 371178 Unique genomic coordinates Making up 10093 groups Consisting of 3693 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144843-chr5-+-73348891-73349388 l43 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 677910 reads mapping to 370887 Unique genomic coordinates Making up 10164 groups Consisting of 3747 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000151196-chr5---145838489-145838989 l45 e 89 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 655032 reads mapping to 356391 Unique genomic coordinates Making up 9714 groups Consisting of 3500 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000141038-chr3-+-151155390-151155890 l45 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 709342 reads mapping to 357686 Unique genomic coordinates Making up 9815 groups Consisting of 3636 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136803-chr2-+-179816291-179816791 l45 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 836845 reads mapping to 373564 Unique genomic coordinates Making up 10219 groups Consisting of 3726 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000131567-chr16---96655239-96656192 l44 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 876102 reads mapping to 356853 Unique genomic coordinates Making up 9700 groups Consisting of 3581 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099576-chr2-+-113203493-113203993 l45 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 844630 reads mapping to 365169 Unique genomic coordinates Making up 9870 groups Consisting of 3600 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144160-chr4---21607094-21607594 l43 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 811024 reads mapping to 383748 Unique genomic coordinates Making up 10537 groups Consisting of 3856 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000105813-chr4-+-137991595-137992095 l45 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 694215 reads mapping to 366451 Unique genomic coordinates Making up 9982 groups Consisting of 3655 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000131102-chr4---82650296-82650796 l43 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 743264 reads mapping to 359329 Unique genomic coordinates Making up 9694 groups Consisting of 3526 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000117932-chr4---60732506-60733297 l43 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 773082 reads mapping to 367744 Unique genomic coordinates Making up 9959 groups Consisting of 3704 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025217-chr18---35105098-35105598 l44 e 98 nr 1000000 chr ENSMUST00000114096-chr9---58837498-58837998 l43 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1048934 reads mapping to 369993 Unique genomic coordinates Making up 10228 groups Consisting of 3641 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030826-chr4-+-149499199-149499699 l45 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 712962 reads mapping to 356820 Unique genomic coordinates Making up 9704 groups Consisting of 3584 clusters