Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028395-chr2-+-79153350-79154500 l43 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 832018 reads mapping to 385682 Unique genomic coordinates Making up 10793 groups Consisting of 3172 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099401-chr19---45307178-45310301 l44 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 835300 reads mapping to 403494 Unique genomic coordinates Making up 11263 groups Consisting of 3310 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000061852-chr2-+-3375463-3381402 l41 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 863202 reads mapping to 434068 Unique genomic coordinates Making up 11852 groups Consisting of 3666 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000092070-chr18-+-12607541-12609503 l44 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 933818 reads mapping to 406602 Unique genomic coordinates Making up 11149 groups Consisting of 3336 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024596-chr17---12867612-12868704 l44 e 4 nr 1000000 chr ENSMUST00000045620-chr9-+-15348483-15349704 l43 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1061091 reads mapping to 417757 Unique genomic coordinates Making up 11570 groups Consisting of 3526 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144704-chr2---30514133-30515905 l43 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 997344 reads mapping to 427941 Unique genomic coordinates Making up 11814 groups Consisting of 3556 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142861-chr2-+-126911199-126913606 l45 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 788175 reads mapping to 406625 Unique genomic coordinates Making up 11295 groups Consisting of 3343 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000172818-chr17---64657463-64659507 l44 e 7 nr 1000000 chr ENSMUST00000109744-chr8-+-87432459-87435607 l43 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1080315 reads mapping to 418919 Unique genomic coordinates Making up 11440 groups Consisting of 3443 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036934-chr2---52100301-52101408 l43 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 853559 reads mapping to 404872 Unique genomic coordinates Making up 11104 groups Consisting of 3333 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000162488-chr15-+-73362749-73364409 l44 e 9 nr 1000000 chr ENSMUST00000041382-chr8---113416689-113420409 l45 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1063957 reads mapping to 397561 Unique genomic coordinates Making up 10939 groups Consisting of 3254 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135225-chr5---109051779-109054610 l45 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 693469 reads mapping to 397071 Unique genomic coordinates Making up 11084 groups Consisting of 3321 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025497-chr18---58312914-58314111 l44 e 11 nr 1000000 chr ENSMUST00000146981-chr6-+-39097567-39098311 l43 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1150058 reads mapping to 400293 Unique genomic coordinates Making up 11135 groups Consisting of 3364 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000132248-chr3---122591686-122593712 l45 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 813191 reads mapping to 416524 Unique genomic coordinates Making up 11698 groups Consisting of 3437 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028475-chr2---84565186-84566813 l43 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 817005 reads mapping to 419825 Unique genomic coordinates Making up 11551 groups Consisting of 3549 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028237-chr2-+-35003511-35005614 l43 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 866513 reads mapping to 420983 Unique genomic coordinates Making up 11561 groups Consisting of 3500 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148770-chr11---99192057-99193115 l44 e 15 nr 1000000 chr ENSMUST00000082370-chr5---88124553-88127615 l43 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1229925 reads mapping to 419939 Unique genomic coordinates Making up 11579 groups Consisting of 3475 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000055930-chr2-+-68568623-68571516 l43 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 880559 reads mapping to 398044 Unique genomic coordinates Making up 11046 groups Consisting of 3341 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125223-chr2-+-145937740-145938817 l45 e 17 nr 1000000 chr ENSMUST00000046502-chr9---106614163-106616417 l45 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1026571 reads mapping to 420578 Unique genomic coordinates Making up 11682 groups Consisting of 3510 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000164316-chr19---41321896-41323018 l44 e 18 nr 1000000 chr ENSMUST00000070117-chr9---114522242-114523418 l45 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1022678 reads mapping to 403515 Unique genomic coordinates Making up 11272 groups Consisting of 3248 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000089726-chr2---103983230-103989719 l45 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 872234 reads mapping to 428538 Unique genomic coordinates Making up 11944 groups Consisting of 3562 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000160801-chr13-+-95786782-95789420 l44 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 998278 reads mapping to 391661 Unique genomic coordinates Making up 10892 groups Consisting of 3265 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000108182-chr3---35791900-35795121 l43 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 830612 reads mapping to 386769 Unique genomic coordinates Making up 10653 groups Consisting of 3119 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000069245-chr18-+-44146935-44148022 l44 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 875170 reads mapping to 408776 Unique genomic coordinates Making up 11317 groups Consisting of 3350 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025081-chr18-+-5765719-5768523 l42 e 23 nr 1000000 chr ENSMUST00000062474-chr9---121823474-121825423 l45 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1029655 reads mapping to 414653 Unique genomic coordinates Making up 11487 groups Consisting of 3391 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113967-chr19-+-3803895-3806324 l42 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 888167 reads mapping to 429054 Unique genomic coordinates Making up 11787 groups Consisting of 3473 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114308-chr2---25165395-25167425 l43 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 961143 reads mapping to 407176 Unique genomic coordinates Making up 11160 groups Consisting of 3363 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144437-chr10-+-12833464-12834526 l44 e 26 nr 1000000 chr ENSMUST00000054702-chr13---61670898-61671426 l44 e 26 nr 1500000 chr ENSMUST00000034226-chr8---97124897-97125626 l43 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1595542 reads mapping to 426235 Unique genomic coordinates Making up 11918 groups Consisting of 3541 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000017147-chr2-+-164115004-164117227 l45 e 27 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 755334 reads mapping to 391399 Unique genomic coordinates Making up 10734 groups Consisting of 3248 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159481-chr3-+-137808751-137811428 l45 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 934369 reads mapping to 404829 Unique genomic coordinates Making up 11331 groups Consisting of 3425 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133664-chr2-+-11704768-11708429 l43 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 986577 reads mapping to 399382 Unique genomic coordinates Making up 11045 groups Consisting of 3286 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113200-chr2---32791456-32792530 l43 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 919665 reads mapping to 421815 Unique genomic coordinates Making up 11801 groups Consisting of 3459 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000056962-chr16-+-17646563-17650831 l44 e 31 nr 1000000 chr ENSMUST00000035014-chr9---116040163-116041331 l45 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1049172 reads mapping to 418996 Unique genomic coordinates Making up 11553 groups Consisting of 3507 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000108831-chr2---180962320-180976732 l45 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 797439 reads mapping to 408344 Unique genomic coordinates Making up 11325 groups Consisting of 3472 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036069-chr19---23433140-23434233 l44 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 877285 reads mapping to 407529 Unique genomic coordinates Making up 11273 groups Consisting of 3428 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000089948-chr3-+-153920212-153922534 l45 e 34 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 790609 reads mapping to 400427 Unique genomic coordinates Making up 11038 groups Consisting of 3286 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028926-chr2---148519721-148525235 l45 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 859454 reads mapping to 415309 Unique genomic coordinates Making up 11593 groups Consisting of 3456 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029569-chr3---116372387-116377136 l45 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 809145 reads mapping to 403957 Unique genomic coordinates Making up 11228 groups Consisting of 3330 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029445-chr3-+-102865797-102871837 l45 e 37 nr 1000000 chr ENSMUST00000084030-chr8---26285114-26286237 l43 e 37 nr 1500000 chr ENSMUST00000035170-chr9---104097853-104098937 l45 e 37 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1556181 reads mapping to 397462 Unique genomic coordinates Making up 11153 groups Consisting of 3277 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169835-chr3---86709307-86710638 l43 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 853647 reads mapping to 394707 Unique genomic coordinates Making up 10901 groups Consisting of 3314 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000137903-chr4---40150810-40153639 l43 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 771845 reads mapping to 412154 Unique genomic coordinates Making up 11324 groups Consisting of 3409 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000040128-chr2---126283479-126284540 l45 e 40 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 777141 reads mapping to 404497 Unique genomic coordinates Making up 11297 groups Consisting of 3369 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000141509-chr2-+-25123084-25123641 l43 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 985952 reads mapping to 432750 Unique genomic coordinates Making up 12079 groups Consisting of 3532 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165956-chr3-+-36062478-36065142 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 812357 reads mapping to 395914 Unique genomic coordinates Making up 10981 groups Consisting of 3222 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000097323-chr17-+-41088204-41090343 l44 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 982785 reads mapping to 423047 Unique genomic coordinates Making up 11697 groups Consisting of 3513 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000115764-chr17---6853659-6855444 l42 e 44 nr 1000000 chr ENSMUST00000113159-chrX---132160558-132162244 l45 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1003876 reads mapping to 415034 Unique genomic coordinates Making up 11433 groups Consisting of 3469 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000108856-chr2-+-180747272-180752245 l45 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 788677 reads mapping to 416971 Unique genomic coordinates Making up 11498 groups Consisting of 3479 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109631-chr2---155755249-155756046 l45 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 913856 reads mapping to 432681 Unique genomic coordinates Making up 12029 groups Consisting of 3567 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000038341-chr2-+-118455139-118458747 l45 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 791707 reads mapping to 400534 Unique genomic coordinates Making up 11118 groups Consisting of 3289 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000143070-chr4-+-127152178-127153048 l45 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 719365 reads mapping to 397629 Unique genomic coordinates Making up 11113 groups Consisting of 3324 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026227-chr19-+-45081048-45085549 l44 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 862689 reads mapping to 411444 Unique genomic coordinates Making up 11434 groups Consisting of 3396 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000095585-chr13---81582845-81584850 l44 e 50 nr 1000000 chr ENSMUST00000013220-chr9---14346410-14353750 l43 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1060428 reads mapping to 418200 Unique genomic coordinates Making up 11546 groups Consisting of 3494 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028278-chr2-+-61598193-61599651 l43 e 51 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 901215 reads mapping to 387552 Unique genomic coordinates Making up 10653 groups Consisting of 3213 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135297-chr2-+-72817481-72818152 l43 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 855332 reads mapping to 421769 Unique genomic coordinates Making up 11581 groups Consisting of 3489 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000041830-chr2-+-30677382-30678553 l43 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 865935 reads mapping to 411479 Unique genomic coordinates Making up 11322 groups Consisting of 3493 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000040513-chr14-+-102310716-102314054 l46 e 54 nr 1000000 chr ENSMUST00000091188-chrY---668264-669454 l39 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 999941 reads mapping to 426017 Unique genomic coordinates Making up 11908 groups Consisting of 3598 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125373-chr15-+-98637463-98638155 l44 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 992966 reads mapping to 406294 Unique genomic coordinates Making up 11258 groups Consisting of 3323 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000156049-chr2---34847779-34848856 l43 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 816292 reads mapping to 412567 Unique genomic coordinates Making up 11514 groups Consisting of 3489 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028225-chr2---34720547-34723057 l43 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 826996 reads mapping to 423074 Unique genomic coordinates Making up 11830 groups Consisting of 3532 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000174066-chr2-+-26487624-26488758 l43 e 58 nr 1000000 chr ENSMUST00000167773-chr9-+-64900352-64904258 l43 e 58 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1081097 reads mapping to 397122 Unique genomic coordinates Making up 10987 groups Consisting of 3269 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109279-chr2---165233822-165234959 l45 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 757970 reads mapping to 394853 Unique genomic coordinates Making up 10998 groups Consisting of 3267 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000070453-chr11-+-61497593-61500360 l44 e 60 nr 1000000 chr ENSMUST00000138021-chr2---34228075-34228660 l43 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1489468 reads mapping to 401704 Unique genomic coordinates Making up 10996 groups Consisting of 3310 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000126704-chr2---150414139-150416361 l45 e 61 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 799102 reads mapping to 401274 Unique genomic coordinates Making up 11156 groups Consisting of 3357 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113532-chr2-+-31258673-31263162 l43 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 829614 reads mapping to 421337 Unique genomic coordinates Making up 11682 groups Consisting of 3502 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029848-chr3-+-145204054-145205163 l45 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 703156 reads mapping to 402588 Unique genomic coordinates Making up 11101 groups Consisting of 3398 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026925-chr2---5794289-5795964 l41 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 849091 reads mapping to 418380 Unique genomic coordinates Making up 11620 groups Consisting of 3451 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000088924-chr2-+-154087140-154091765 l45 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 850610 reads mapping to 401358 Unique genomic coordinates Making up 11129 groups Consisting of 3381 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107745-chr3---80512800-80515266 l43 e 66 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 790619 reads mapping to 369242 Unique genomic coordinates Making up 10243 groups Consisting of 2989 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125859-chr19-+-3888523-3894367 l42 e 67 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 989344 reads mapping to 397442 Unique genomic coordinates Making up 11099 groups Consisting of 3305 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025962-chr19-+-38775810-38777068 l44 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 977107 reads mapping to 422821 Unique genomic coordinates Making up 11701 groups Consisting of 3493 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000053917-chr18---9318907-9320069 l42 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 884729 reads mapping to 401355 Unique genomic coordinates Making up 10984 groups Consisting of 3351 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173431-chr3-+-34564165-34564870 l43 e 70 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 930928 reads mapping to 390928 Unique genomic coordinates Making up 10785 groups Consisting of 3282 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024823-chr17---30729811-30731671 l44 e 71 nr 1000000 chr ENSMUST00000064476-chrX-+-130737013-130738771 l45 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1008381 reads mapping to 397927 Unique genomic coordinates Making up 10927 groups Consisting of 3251 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000103122-chr2---157971527-157972172 l45 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 890673 reads mapping to 415349 Unique genomic coordinates Making up 11436 groups Consisting of 3446 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000100446-chr2---5282535-5283673 l41 e 73 nr 1000000 chr ENSMUST00000161731-chr2-+-113432744-113433873 l45 e 73 nr 1500000 chr ENSMUST00000033827-chr8-+-13412549-13413673 l43 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1636120 reads mapping to 402174 Unique genomic coordinates Making up 11215 groups Consisting of 3461 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000105912-chr4-+-132744493-132746674 l45 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 842093 reads mapping to 414981 Unique genomic coordinates Making up 11564 groups Consisting of 3430 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000145910-chr17---79049253-79055675 l44 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 979137 reads mapping to 416323 Unique genomic coordinates Making up 11481 groups Consisting of 3539 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000103042-chr2-+-181419997-181422776 l45 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 790806 reads mapping to 393138 Unique genomic coordinates Making up 10861 groups Consisting of 3245 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000043784-chr4-+-46035767-46036877 l43 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 800587 reads mapping to 402717 Unique genomic coordinates Making up 11184 groups Consisting of 3363 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000162490-chr2-+-36002623-36004078 l43 e 78 nr 1000000 chr ENSMUST00000112588-chrX-+-148700600-148709078 l45 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1008100 reads mapping to 432131 Unique genomic coordinates Making up 12062 groups Consisting of 3658 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036584-chr19---34895090-34896879 l44 e 79 nr 1000000 chr ENSMUST00000162900-chr6-+-89090999-89091579 l43 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1123093 reads mapping to 400222 Unique genomic coordinates Making up 11217 groups Consisting of 3381 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099823-chr2---88263245-88264180 l43 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 871445 reads mapping to 415057 Unique genomic coordinates Making up 11373 groups Consisting of 3395 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025681-chr19-+-6319579-6323381 l42 e 81 nr 1000000 chr ENSMUST00000028233-chr2---34894231-34895781 l43 e 81 nr 1500000 chr ENSMUST00000028233-chr2---34894231-34895781 l43 e 81 nr 2000000 chr ENSMUST00000028233-chr2---34894231-34895781 l43 e 81 nr 2500000 chr ENSMUST00000028233-chr2---34894231-34895781 l43 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 2964096 reads mapping to 391042 Unique genomic coordinates Making up 10900 groups Consisting of 3270 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000152415-chr2-+-28048512-28049482 l43 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 817909 reads mapping to 409676 Unique genomic coordinates Making up 11500 groups Consisting of 3424 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102790-chr4---98444455-98447383 l43 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 822720 reads mapping to 423232 Unique genomic coordinates Making up 11793 groups Consisting of 3528 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125327-chr2---126624405-126627384 l45 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 901394 reads mapping to 389442 Unique genomic coordinates Making up 10679 groups Consisting of 3199 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099163-chr3---30828218-30829485 l43 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 792496 reads mapping to 418818 Unique genomic coordinates Making up 11493 groups Consisting of 3358 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148753-chr4-+-73914641-73915586 l43 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 789444 reads mapping to 406909 Unique genomic coordinates Making up 11252 groups Consisting of 3379 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000155979-chr2-+-70411626-70415187 l43 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 837754 reads mapping to 418244 Unique genomic coordinates Making up 11634 groups Consisting of 3522 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029297-chr3---50168858-50176788 l43 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 835896 reads mapping to 405145 Unique genomic coordinates Making up 11262 groups Consisting of 3320 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169685-chr18---77801871-77802689 l44 e 89 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 925123 reads mapping to 385391 Unique genomic coordinates Making up 10736 groups Consisting of 3341 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114076-chr16---91068777-91069390 l44 e 90 nr 1000000 chr ENSMUST00000161602-chr4---108758432-108760590 l45 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1306186 reads mapping to 397720 Unique genomic coordinates Making up 11021 groups Consisting of 3228 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163360-chr17---35133681-35137691 l44 e 91 nr 1000000 chr ENSMUST00000168989-chr18---15219777-15222091 l44 e 91 nr 1500000 chr ENSMUST00000031391-chr5-+-123820527-123824091 l45 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1717033 reads mapping to 431199 Unique genomic coordinates Making up 11767 groups Consisting of 3502 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030806-chr4---148607843-148613092 l45 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 984619 reads mapping to 402503 Unique genomic coordinates Making up 11244 groups Consisting of 3346 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138751-chr2-+-132471617-132472293 l45 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 933693 reads mapping to 418419 Unique genomic coordinates Making up 11525 groups Consisting of 3472 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000009617-chr3---107241221-107242894 l45 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 817673 reads mapping to 427397 Unique genomic coordinates Making up 11799 groups Consisting of 3511 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000066728-chr3-+-122450307-122451895 l45 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 806506 reads mapping to 394078 Unique genomic coordinates Making up 11004 groups Consisting of 3225 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039419-chr3---59120657-59124796 l43 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 770871 reads mapping to 419010 Unique genomic coordinates Making up 11658 groups Consisting of 3555 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029131-chr2---155331191-155332797 l45 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 768418 reads mapping to 405008 Unique genomic coordinates Making up 11314 groups Consisting of 3430 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000149965-chr2-+-133277024-133279098 l45 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 839188 reads mapping to 412541 Unique genomic coordinates Making up 11473 groups Consisting of 3528 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000164954-chr3---32372101-32373299 l43 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 944943 reads mapping to 409861 Unique genomic coordinates Making up 11334 groups Consisting of 3340 clusters