Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035471-chr17-+-68132834-68136000 l44 e 0 nr 1000000 chr ENSMUST00000149771-chr9-+-100851526-100852700 l45 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1066212 reads mapping to 375463 Unique genomic coordinates Making up 10460 groups Consisting of 3203 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000137975-chr3-+-89070561-89071001 l43 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 779616 reads mapping to 379407 Unique genomic coordinates Making up 10574 groups Consisting of 3143 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035471-chr17-+-68101222-68103702 l44 e 2 nr 1000000 chr ENSMUST00000163694-chr9-+-59522336-59523502 l43 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1031819 reads mapping to 420008 Unique genomic coordinates Making up 11474 groups Consisting of 3578 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000172791-chr2---12125858-12126903 l43 e 3 nr 1000000 chr ENSMUST00000113374-chr9-+-78175396-78177403 l43 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1130419 reads mapping to 396779 Unique genomic coordinates Making up 10684 groups Consisting of 3368 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091146-chr2-+-29579793-29580904 l43 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 937326 reads mapping to 414521 Unique genomic coordinates Making up 11434 groups Consisting of 3591 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039894-chr13---14131305-14131905 l44 e 5 nr 1000000 chr ENSMUST00000044523-chr18---43699635-43700805 l44 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1411277 reads mapping to 414337 Unique genomic coordinates Making up 11530 groups Consisting of 3484 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000150459-chr10-+-83224163-83225506 l44 e 6 nr 1000000 chr ENSMUST00000025078-chr18---4338995-4341306 l42 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1453319 reads mapping to 388670 Unique genomic coordinates Making up 10624 groups Consisting of 3188 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000131246-chr11-+-86298232-86299607 l44 e 7 nr 1000000 chr ENSMUST00000040260-chr3-+-116587525-116588707 l45 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1306458 reads mapping to 407917 Unique genomic coordinates Making up 11139 groups Consisting of 3408 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000011934-chr2---76805953-76808508 l43 e 8 nr 1000000 chr ENSMUST00000112686-chr6-+-120715930-120721208 l45 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1155951 reads mapping to 392084 Unique genomic coordinates Making up 10830 groups Consisting of 3301 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000149293-chr15---38422446-38425609 l44 e 9 nr 1000000 chr ENSMUST00000042701-chr5---34516536-34520909 l43 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1207875 reads mapping to 399110 Unique genomic coordinates Making up 10948 groups Consisting of 3454 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110227-chr2---130903157-130907810 l45 e 10 nr 1000000 chr ENSMUST00000049545-chr5-+-35621215-35624410 l43 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1288098 reads mapping to 383774 Unique genomic coordinates Making up 10619 groups Consisting of 3201 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035860-chr3---40411424-40412711 l43 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 986068 reads mapping to 400157 Unique genomic coordinates Making up 10862 groups Consisting of 3472 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000048646-chr15-+-35804817-35810212 l44 e 12 nr 1000000 chr ENSMUST00000111878-chr6---137462299-137463812 l45 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1324291 reads mapping to 412649 Unique genomic coordinates Making up 11076 groups Consisting of 3395 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000041314-chr18-+-35758271-35758913 l44 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 924627 reads mapping to 410254 Unique genomic coordinates Making up 11193 groups Consisting of 3438 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000060092-chr2-+-5943829-5945014 l41 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 987537 reads mapping to 410945 Unique genomic coordinates Making up 11257 groups Consisting of 3510 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025897-chr19-+-6350680-6355615 l42 e 15 nr 1000000 chr ENSMUST00000095267-chr8-+-73221638-73224515 l43 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1088586 reads mapping to 419477 Unique genomic coordinates Making up 11390 groups Consisting of 3620 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026209-chr19---43923766-43925316 l44 e 16 nr 1000000 chr ENSMUST00000004327-chrX---71654822-71658316 l43 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1022241 reads mapping to 404512 Unique genomic coordinates Making up 10971 groups Consisting of 3461 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025215-chr18---35476996-35478117 l44 e 17 nr 1000000 chr ENSMUST00000031061-chr5---52541448-52542517 l43 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1335912 reads mapping to 414124 Unique genomic coordinates Making up 11381 groups Consisting of 3549 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000111955-chr14-+-34132889-34133618 l44 e 18 nr 1000000 chr ENSMUST00000037096-chr2-+-156163811-156165518 l45 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1404426 reads mapping to 408367 Unique genomic coordinates Making up 11180 groups Consisting of 3543 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000041772-chr18-+-50036837-50039519 l44 e 19 nr 1000000 chr ENSMUST00000140133-chr9-+-69608953-69609519 l43 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1035942 reads mapping to 417840 Unique genomic coordinates Making up 11512 groups Consisting of 3542 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028607-chr2---103603098-103607520 l45 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 908623 reads mapping to 383340 Unique genomic coordinates Making up 10456 groups Consisting of 3262 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000128595-chr16-+-25316838-25318321 l44 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 954407 reads mapping to 374902 Unique genomic coordinates Making up 10221 groups Consisting of 3173 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102838-chr11---30006785-30011422 l44 e 22 nr 1000000 chr ENSMUST00000145720-chr3---108709479-108711822 l45 e 22 nr 1500000 chr ENSMUST00000032818-chr7-+-29519796-29521722 l43 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1655871 reads mapping to 410244 Unique genomic coordinates Making up 11284 groups Consisting of 3572 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113331-chr2-+-32230505-32233823 l43 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 840061 reads mapping to 409868 Unique genomic coordinates Making up 11196 groups Consisting of 3465 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022894-chr15---36704494-36706624 l44 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 987544 reads mapping to 414681 Unique genomic coordinates Making up 11463 groups Consisting of 3466 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165643-chr18---38117085-38120125 l44 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 983422 reads mapping to 394009 Unique genomic coordinates Making up 10798 groups Consisting of 3300 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000057942-chr18---67017369-67020126 l44 e 26 nr 1000000 chr ENSMUST00000059555-chr9-+-55042294-55043826 l43 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1034222 reads mapping to 422215 Unique genomic coordinates Making up 11662 groups Consisting of 3517 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028917-chr2-+-144425633-144426327 l45 e 27 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 820458 reads mapping to 387378 Unique genomic coordinates Making up 10524 groups Consisting of 3267 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110457-chr15-+-25741376-25743428 l44 e 28 nr 1000000 chr ENSMUST00000121086-chr4---74334011-74335228 l43 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1360949 reads mapping to 397761 Unique genomic coordinates Making up 10985 groups Consisting of 3345 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000037181-chr12---68321457-68323529 l44 e 29 nr 1000000 chr ENSMUST00000167058-chr13---103576897-103578029 l46 e 29 nr 1500000 chr ENSMUST00000153640-chr7-+-129214716-129216029 l45 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1590828 reads mapping to 394715 Unique genomic coordinates Making up 10744 groups Consisting of 3285 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000100167-chr16-+-14471531-14475830 l44 e 30 nr 1000000 chr ENSMUST00000056740-chr9-+-54179184-54180330 l43 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1050123 reads mapping to 419148 Unique genomic coordinates Making up 11583 groups Consisting of 3604 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165227-chr19-+-34150895-34152031 l44 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 991337 reads mapping to 422739 Unique genomic coordinates Making up 11340 groups Consisting of 3471 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000018353-chr2-+-163924933-163926832 l45 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 877718 reads mapping to 395677 Unique genomic coordinates Making up 10964 groups Consisting of 3379 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035342-chr15---94191684-94193533 l44 e 33 nr 1000000 chr ENSMUST00000137018-chr5-+-76966223-76970133 l43 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1201569 reads mapping to 405363 Unique genomic coordinates Making up 11172 groups Consisting of 3424 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026710-chr16-+-87478871-87480534 l44 e 34 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 946607 reads mapping to 397185 Unique genomic coordinates Making up 10883 groups Consisting of 3340 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000003509-chr2---13713881-13715435 l43 e 35 nr 1000000 chr ENSMUST00000170183-chrX---158277231-158282735 l45 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1008267 reads mapping to 403506 Unique genomic coordinates Making up 11165 groups Consisting of 3405 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121869-chr16---48944376-48946236 l44 e 36 nr 1000000 chr ENSMUST00000144881-chrX-+-97689694-97694736 l43 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1015721 reads mapping to 406217 Unique genomic coordinates Making up 11161 groups Consisting of 3469 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166581-chr3-+-82831944-82837537 l43 e 37 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 829343 reads mapping to 391416 Unique genomic coordinates Making up 10760 groups Consisting of 3353 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166957-chr15-+-44366760-44369538 l44 e 38 nr 1000000 chr ENSMUST00000144568-chr6---8457059-8459138 l41 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1207379 reads mapping to 394277 Unique genomic coordinates Making up 10810 groups Consisting of 3323 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166783-chr18---62016156-62017339 l44 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 942469 reads mapping to 406052 Unique genomic coordinates Making up 11171 groups Consisting of 3413 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000115995-chr19-+-10126192-10131540 l44 e 40 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 942416 reads mapping to 398384 Unique genomic coordinates Making up 11038 groups Consisting of 3377 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000116584-chr16---84727229-84728341 l44 e 41 nr 1000000 chr ENSMUST00000098556-chr9-+-75190792-75191541 l43 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1031285 reads mapping to 419397 Unique genomic coordinates Making up 11507 groups Consisting of 3490 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000111493-chr2---90279514-90281442 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 841609 reads mapping to 382653 Unique genomic coordinates Making up 10654 groups Consisting of 3208 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133262-chr2-+-160471716-160475843 l45 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 807389 reads mapping to 406073 Unique genomic coordinates Making up 11224 groups Consisting of 3412 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000066646-chr19-+-7342791-7346544 l42 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 908400 reads mapping to 400743 Unique genomic coordinates Making up 11111 groups Consisting of 3360 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000129723-chr2-+-25150894-25154445 l43 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 931882 reads mapping to 413421 Unique genomic coordinates Making up 11187 groups Consisting of 3456 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000046288-chr17-+-31663755-31665846 l44 e 46 nr 1000000 chr ENSMUST00000131438-chr8-+-111695221-111696446 l45 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1070072 reads mapping to 414229 Unique genomic coordinates Making up 11279 groups Consisting of 3457 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000075510-chr17---56702362-56707547 l44 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 930445 reads mapping to 393464 Unique genomic coordinates Making up 10768 groups Consisting of 3322 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000017799-chr2-+-164894629-164898448 l45 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 813216 reads mapping to 395311 Unique genomic coordinates Making up 10973 groups Consisting of 3407 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161371-chr10-+-122322764-122323349 l46 e 49 nr 1000000 chr ENSMUST00000153734-chr11-+-90048998-90050049 l44 e 49 nr 1500000 chr ENSMUST00000119685-chr5-+-149998784-150000549 l45 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1671752 reads mapping to 405445 Unique genomic coordinates Making up 11183 groups Consisting of 3444 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000056641-chr2-+-24259402-24261850 l43 e 50 nr 1000000 chr ENSMUST00000124575-chr6---148616167-148617250 l45 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1152294 reads mapping to 410057 Unique genomic coordinates Making up 11216 groups Consisting of 3554 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159036-chr16-+-29601798-29602851 l44 e 51 nr 1000000 chr ENSMUST00000171357-chr8-+-26820645-26821751 l43 e 51 nr 1500000 chr ENSMUST00000101670-chrX-+-23380395-23383151 l43 e 51 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1553532 reads mapping to 382604 Unique genomic coordinates Making up 10529 groups Consisting of 3236 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000128855-chr2---34561040-34562852 l43 e 52 nr 1000000 chr ENSMUST00000166114-chr5---16732014-16733752 l43 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1421039 reads mapping to 420057 Unique genomic coordinates Making up 11476 groups Consisting of 3604 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110846-chr2-+-118631624-118632653 l45 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 894594 reads mapping to 411365 Unique genomic coordinates Making up 11251 groups Consisting of 3463 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166219-chr18---80431688-80432754 l44 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 873365 reads mapping to 416744 Unique genomic coordinates Making up 11474 groups Consisting of 3529 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000049714-chr11-+-83832362-83833955 l44 e 55 nr 1000000 chr ENSMUST00000049714-chr11-+-83832362-83833955 l44 e 55 nr 1500000 chr ENSMUST00000114170-chr2-+-25733377-25734055 l43 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1871920 reads mapping to 390566 Unique genomic coordinates Making up 10671 groups Consisting of 3211 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000086876-chr17---55826587-55827756 l44 e 56 nr 1000000 chr ENSMUST00000170416-chr8---47118615-47120356 l43 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1358656 reads mapping to 409895 Unique genomic coordinates Making up 11079 groups Consisting of 3515 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000027961-chr2---3419266-3420557 l41 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 882393 reads mapping to 417027 Unique genomic coordinates Making up 11490 groups Consisting of 3624 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000060618-chr2---3376529-3377658 l41 e 58 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 954197 reads mapping to 385693 Unique genomic coordinates Making up 10618 groups Consisting of 3322 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000040381-chr2---164825857-164828959 l45 e 59 nr 1000000 chr ENSMUST00000168164-chr8---13104275-13105459 l43 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1332420 reads mapping to 392971 Unique genomic coordinates Making up 10767 groups Consisting of 3450 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028583-chr2-+-109735893-109741160 l45 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 992679 reads mapping to 392756 Unique genomic coordinates Making up 10746 groups Consisting of 3359 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000132669-chr2---173414123-173416461 l45 e 61 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 903331 reads mapping to 395264 Unique genomic coordinates Making up 10827 groups Consisting of 3428 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022875-chr15-+-27482944-27484062 l44 e 62 nr 1000000 chr ENSMUST00000102837-chr4---73395247-73396362 l43 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1328972 reads mapping to 406979 Unique genomic coordinates Making up 11234 groups Consisting of 3367 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000003642-chr17---46771859-46774463 l44 e 63 nr 1000000 chr ENSMUST00000098757-chr8---60905997-60907163 l43 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1069827 reads mapping to 391663 Unique genomic coordinates Making up 10746 groups Consisting of 3276 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133112-chr18---12376087-12382164 l44 e 64 nr 1000000 chr ENSMUST00000048250-chrX-+-82869181-82870264 l43 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1162412 reads mapping to 409397 Unique genomic coordinates Making up 11278 groups Consisting of 3480 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099902-chr2---86056915-86057865 l43 e 65 nr 1000000 chr ENSMUST00000115393-chrX---19738554-19740165 l43 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1049449 reads mapping to 391030 Unique genomic coordinates Making up 10756 groups Consisting of 3245 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106448-chr4-+-116753663-116754766 l45 e 66 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 669036 reads mapping to 355934 Unique genomic coordinates Making up 9793 groups Consisting of 2893 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000074653-chr18---77872020-77874567 l44 e 67 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 866585 reads mapping to 402556 Unique genomic coordinates Making up 11029 groups Consisting of 3461 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000005975-chr17---57383170-57385268 l44 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 997784 reads mapping to 412550 Unique genomic coordinates Making up 11420 groups Consisting of 3435 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000160970-chr19---47875853-47876969 l44 e 69 nr 1000000 chr ENSMUST00000039509-chr9---67211769-67212769 l43 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1099225 reads mapping to 382406 Unique genomic coordinates Making up 10615 groups Consisting of 3183 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163874-chr3---58982845-58984470 l43 e 70 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 856419 reads mapping to 375115 Unique genomic coordinates Making up 10513 groups Consisting of 3191 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000015620-chr17-+-34766478-34770071 l44 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 951690 reads mapping to 396045 Unique genomic coordinates Making up 10934 groups Consisting of 3325 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025695-chr19---6231770-6235872 l42 e 72 nr 1000000 chr ENSMUST00000101405-chr6---50150223-50153872 l43 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1200054 reads mapping to 411652 Unique genomic coordinates Making up 11299 groups Consisting of 3544 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000081079-chr19-+-43791440-43792573 l44 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 900166 reads mapping to 399819 Unique genomic coordinates Making up 11051 groups Consisting of 3368 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000137586-chr2---26109775-26113074 l43 e 74 nr 1000000 chr ENSMUST00000129704-chr5---141144476-141145574 l45 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1324771 reads mapping to 407589 Unique genomic coordinates Making up 11169 groups Consisting of 3409 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099490-chr13-+-55394419-55395575 l44 e 75 nr 1000000 chr ENSMUST00000075806-chr16---29260503-29261575 l44 e 75 nr 1500000 chr ENSMUST00000075806-chr16---29260503-29261575 l44 e 75 nr 2000000 chr ENSMUST00000117556-chr6---38117591-38118775 l43 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 2151065 reads mapping to 402045 Unique genomic coordinates Making up 11139 groups Consisting of 3411 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028178-chr2---58147837-58149076 l43 e 76 nr 1000000 chr ENSMUST00000028178-chr2---58147837-58149076 l43 e 76 nr 1500000 chr ENSMUST00000028178-chr2---58147837-58149076 l43 e 76 nr 2000000 chr ENSMUST00000148538-chr7-+-74148726-74149876 l43 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 2202672 reads mapping to 388124 Unique genomic coordinates Making up 10558 groups Consisting of 3270 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000140913-chr3-+-121828539-121830377 l45 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 904311 reads mapping to 393001 Unique genomic coordinates Making up 10826 groups Consisting of 3366 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000137894-chr18---60765537-60767178 l44 e 78 nr 1000000 chr ENSMUST00000097504-chr18---82779497-82780578 l44 e 78 nr 1500000 chr ENSMUST00000112414-chr6-+-124999707-125001878 l45 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1744599 reads mapping to 433905 Unique genomic coordinates Making up 11770 groups Consisting of 3722 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025205-chr18-+-36159777-36160779 l44 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 906258 reads mapping to 394691 Unique genomic coordinates Making up 10966 groups Consisting of 3376 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169582-chr16-+-44198517-44199780 l44 e 80 nr 1000000 chr ENSMUST00000165771-chr7---93376190-93380280 l43 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1409563 reads mapping to 413522 Unique genomic coordinates Making up 11329 groups Consisting of 3504 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028233-chr2---34894231-34895781 l43 e 81 nr 1000000 chr ENSMUST00000169847-chr5---72825974-72827181 l43 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1209479 reads mapping to 386114 Unique genomic coordinates Making up 10693 groups Consisting of 3287 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000122856-chr16-+-10629638-10631682 l44 e 82 nr 1000000 chr ENSMUST00000035057-chr9-+-110138720-110142682 l45 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1048882 reads mapping to 412880 Unique genomic coordinates Making up 11281 groups Consisting of 3486 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000001927-chr17-+-75695064-75696183 l44 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 953807 reads mapping to 414695 Unique genomic coordinates Making up 11308 groups Consisting of 3492 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000117223-chr3---33976356-33980184 l43 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 833477 reads mapping to 379756 Unique genomic coordinates Making up 10522 groups Consisting of 3170 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000042556-chr10---77635626-77646285 l44 e 85 nr 1000000 chr ENSMUST00000170534-chr14---9087208-9090385 l42 e 85 nr 1500000 chr ENSMUST00000110836-chr5-+-140273468-140278285 l45 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1815627 reads mapping to 411295 Unique genomic coordinates Making up 11130 groups Consisting of 3455 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091884-chr18---61314182-61315586 l44 e 86 nr 1000000 chr ENSMUST00000165709-chr4-+-106088073-106089186 l45 e 86 nr 1500000 chr ENSMUST00000156452-chrX-+-68560375-68563486 l43 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1679973 reads mapping to 412709 Unique genomic coordinates Making up 11247 groups Consisting of 3530 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025602-chr19-+-16607703-16608887 l44 e 87 nr 1000000 chr ENSMUST00000145784-chr9---55105784-55107787 l43 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1093173 reads mapping to 419068 Unique genomic coordinates Making up 11494 groups Consisting of 3576 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000046227-chr2---24656527-24662388 l43 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 970558 reads mapping to 401233 Unique genomic coordinates Making up 10973 groups Consisting of 3420 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169433-chr3-+-94166366-94168489 l43 e 89 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 828799 reads mapping to 380165 Unique genomic coordinates Making up 10314 groups Consisting of 3272 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025968-chr19-+-39634849-39635990 l44 e 90 nr 1000000 chr ENSMUST00000166168-chr9---60524387-60525590 l43 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1151508 reads mapping to 391256 Unique genomic coordinates Making up 10595 groups Consisting of 3323 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000151984-chr2-+-60207550-60209291 l43 e 91 nr 1000000 chr ENSMUST00000031037-chr5---31388479-31389791 l43 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1468481 reads mapping to 408094 Unique genomic coordinates Making up 11252 groups Consisting of 3383 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135110-chr2---130698795-130701992 l45 e 92 nr 1000000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 1500000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 2000000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 2500000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 3000000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 3500000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 nr 4000000 chr ENSMUST00000120437-chr2---173809983-173810192 l45 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 4366094 reads mapping to 393110 Unique genomic coordinates Making up 10750 groups Consisting of 3279 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000095180-chr17---95131929-95133493 l44 e 93 nr 1000000 chr ENSMUST00000055704-chr9---107521528-107523293 l45 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1036302 reads mapping to 414848 Unique genomic coordinates Making up 11359 groups Consisting of 3510 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000145117-chr2---132640867-132641494 l45 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 950321 reads mapping to 422722 Unique genomic coordinates Making up 11475 groups Consisting of 3524 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026196-chr19---43598328-43599095 l44 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 854484 reads mapping to 388465 Unique genomic coordinates Making up 10527 groups Consisting of 3260 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024742-chr17-+-45694944-45698096 l44 e 96 nr 1000000 chr ENSMUST00000034754-chr9-+-69837273-69837996 l43 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1074574 reads mapping to 414813 Unique genomic coordinates Making up 11435 groups Consisting of 3645 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000078027-chr2-+-142042814-142043897 l45 e 97 nr 1000000 chr ENSMUST00000163793-chr9-+-81095756-81097197 l43 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1067534 reads mapping to 392684 Unique genomic coordinates Making up 10696 groups Consisting of 3392 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035874-chr17---67394824-67395998 l44 e 98 nr 1000000 chr ENSMUST00000014421-chr5---90691784-90695098 l43 e 98 nr 1500000 chr ENSMUST00000056124-chr5---110790773-110793398 l45 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1781690 reads mapping to 408028 Unique genomic coordinates Making up 11062 groups Consisting of 3453 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110537-chr2---122129285-122133099 l45 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 983757 reads mapping to 393822 Unique genomic coordinates Making up 10797 groups Consisting of 3220 clusters