Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000149511-chr3---79423489-79428100 l43 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 774230 reads mapping to 279130 Unique genomic coordinates Making up 7426 groups Consisting of 2203 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000095295-chr8---67505550-67508501 l43 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 549413 reads mapping to 281593 Unique genomic coordinates Making up 7504 groups Consisting of 2083 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029510-chr3---106191108-106194602 l45 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 718781 reads mapping to 313295 Unique genomic coordinates Making up 8249 groups Consisting of 2473 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000094894-chr4-+-114282030-114287703 l45 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 809146 reads mapping to 295777 Unique genomic coordinates Making up 7650 groups Consisting of 2342 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000052258-chr5---120908195-120911204 l45 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 671155 reads mapping to 308380 Unique genomic coordinates Making up 8168 groups Consisting of 2477 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039894-chr13---14131305-14131905 l44 e 5 nr 1000000 chr ENSMUST00000047037-chrX---39166627-39168305 l43 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1013417 reads mapping to 308024 Unique genomic coordinates Making up 8182 groups Consisting of 2354 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000150459-chr10-+-83224163-83225506 l44 e 6 nr 1000000 chr ENSMUST00000164135-chrX-+-117512511-117516006 l45 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1014504 reads mapping to 289150 Unique genomic coordinates Making up 7548 groups Consisting of 2183 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000168985-chr14---87406482-87407707 l44 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 925101 reads mapping to 303557 Unique genomic coordinates Making up 7979 groups Consisting of 2375 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000112817-chr5---104304260-104305808 l45 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 806511 reads mapping to 291986 Unique genomic coordinates Making up 7664 groups Consisting of 2244 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114269-chr2-+-25287016-25288109 l43 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 869807 reads mapping to 297836 Unique genomic coordinates Making up 7863 groups Consisting of 2352 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106210-chr3---144364272-144365310 l45 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 937866 reads mapping to 285023 Unique genomic coordinates Making up 7497 groups Consisting of 2183 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000053410-chr7-+-25864054-25868511 l43 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 712565 reads mapping to 298392 Unique genomic coordinates Making up 7766 groups Consisting of 2420 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110538-chr2---122127927-122131512 l45 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 941528 reads mapping to 308159 Unique genomic coordinates Making up 7902 groups Consisting of 2316 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000044492-chr5-+-4032181-4033413 l41 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 658352 reads mapping to 305378 Unique genomic coordinates Making up 8062 groups Consisting of 2404 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133476-chr5---123746384-123747514 l45 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 703041 reads mapping to 305726 Unique genomic coordinates Making up 7970 groups Consisting of 2411 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030638-chr4-+-133875047-133876215 l45 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 768838 reads mapping to 312856 Unique genomic coordinates Making up 8162 groups Consisting of 2496 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000031490-chr5---111237524-111239116 l45 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 714981 reads mapping to 301377 Unique genomic coordinates Making up 7885 groups Consisting of 2375 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091224-chr2---27087593-27088217 l43 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 959797 reads mapping to 308367 Unique genomic coordinates Making up 8148 groups Consisting of 2452 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023072-chr15-+-84142633-84146118 l44 e 18 nr 1000000 chr ENSMUST00000149811-chrX-+-140797908-140800018 l45 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1002215 reads mapping to 304798 Unique genomic coordinates Making up 8032 groups Consisting of 2452 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000037337-chr5-+-54294071-54295619 l43 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 750304 reads mapping to 310538 Unique genomic coordinates Making up 8233 groups Consisting of 2419 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029771-chr3-+-121426455-121427220 l45 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 664616 reads mapping to 285976 Unique genomic coordinates Making up 7482 groups Consisting of 2223 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000103122-chr2---157945361-157946521 l45 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 689381 reads mapping to 278674 Unique genomic coordinates Making up 7316 groups Consisting of 2174 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022641-chr14---69190383-69191822 l44 e 22 nr 1000000 chr ENSMUST00000030627-chr4-+-134449749-134450822 l45 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1177084 reads mapping to 305614 Unique genomic coordinates Making up 8121 groups Consisting of 2446 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000051065-chr6---59302455-59305923 l43 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 598337 reads mapping to 305249 Unique genomic coordinates Making up 7997 groups Consisting of 2416 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000119690-chr2---175053677-175055724 l45 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 703325 reads mapping to 308772 Unique genomic coordinates Making up 8114 groups Consisting of 2433 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000063672-chr4---63155147-63157025 l43 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 708243 reads mapping to 293425 Unique genomic coordinates Making up 7730 groups Consisting of 2287 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000094329-chr2---165119241-165121626 l45 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 732860 reads mapping to 314144 Unique genomic coordinates Making up 8230 groups Consisting of 2413 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161619-chr6-+-125852543-125853627 l45 e 27 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 585421 reads mapping to 288304 Unique genomic coordinates Making up 7557 groups Consisting of 2262 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000134661-chr2-+-118639739-118640728 l45 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 944160 reads mapping to 295736 Unique genomic coordinates Making up 7735 groups Consisting of 2276 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000037181-chr12---68321457-68323529 l44 e 29 nr 1000000 chr ENSMUST00000067485-chr3---115641891-115650129 l45 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1205962 reads mapping to 294462 Unique genomic coordinates Making up 7555 groups Consisting of 2215 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000057135-chr2---120558552-120566430 l45 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 748816 reads mapping to 311720 Unique genomic coordinates Making up 8269 groups Consisting of 2485 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163744-chr4---49817228-49821231 l43 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 700370 reads mapping to 315788 Unique genomic coordinates Making up 8173 groups Consisting of 2365 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133771-chr7-+-73851411-73856132 l43 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 617007 reads mapping to 293796 Unique genomic coordinates Making up 7778 groups Consisting of 2296 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036256-chr19-+-35005545-35006733 l44 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 850756 reads mapping to 302154 Unique genomic coordinates Making up 7954 groups Consisting of 2301 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000146678-chr4-+-88696212-88696934 l43 e 34 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 671129 reads mapping to 296728 Unique genomic coordinates Making up 7779 groups Consisting of 2277 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000160047-chr3-+-135017475-135018535 l45 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 703940 reads mapping to 299925 Unique genomic coordinates Making up 7996 groups Consisting of 2327 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000127478-chr3---108707394-108709036 l45 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 748496 reads mapping to 302797 Unique genomic coordinates Making up 7992 groups Consisting of 2393 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035372-chr7---116870979-116872137 l45 e 37 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 584741 reads mapping to 292166 Unique genomic coordinates Making up 7733 groups Consisting of 2324 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000080953-chr2---69302131-69305838 l43 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 837128 reads mapping to 293707 Unique genomic coordinates Making up 7690 groups Consisting of 2316 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000084097-chr4-+-155205460-155207239 l45 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 659776 reads mapping to 302301 Unique genomic coordinates Making up 7902 groups Consisting of 2311 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000105806-chr4-+-138333809-138337040 l45 e 40 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 672407 reads mapping to 296539 Unique genomic coordinates Making up 7814 groups Consisting of 2353 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000117280-chr4-+-52472530-52474541 l43 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 723429 reads mapping to 311783 Unique genomic coordinates Making up 8116 groups Consisting of 2390 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000073151-chr7-+-20593372-20593942 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 602909 reads mapping to 284515 Unique genomic coordinates Making up 7558 groups Consisting of 2207 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165159-chr7---111216599-111217543 l45 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 571374 reads mapping to 302280 Unique genomic coordinates Making up 8005 groups Consisting of 2362 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000149146-chr4-+-124588751-124595044 l45 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 658854 reads mapping to 298292 Unique genomic coordinates Making up 7921 groups Consisting of 2299 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000126762-chr5---139781446-139782245 l45 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 666485 reads mapping to 308311 Unique genomic coordinates Making up 8052 groups Consisting of 2417 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170933-chr4---108306448-108310046 l45 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 747232 reads mapping to 307902 Unique genomic coordinates Making up 8096 groups Consisting of 2368 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000045607-chr4-+-44376082-44377547 l43 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 650373 reads mapping to 293514 Unique genomic coordinates Making up 7760 groups Consisting of 2315 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000032931-chr7-+-108401544-108402648 l45 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 569251 reads mapping to 294223 Unique genomic coordinates Making up 7810 groups Consisting of 2315 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161371-chr10-+-122322764-122323349 l46 e 49 nr 1000000 chr ENSMUST00000144652-chr2-+-69567249-69567849 l43 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1259302 reads mapping to 301383 Unique genomic coordinates Making up 7990 groups Consisting of 2407 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000029632-chr3---82696501-82701550 l43 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 810108 reads mapping to 305924 Unique genomic coordinates Making up 8065 groups Consisting of 2400 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025739-chr19-+-30145233-30146451 l44 e 51 nr 1000000 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 1171195 reads mapping to 285291 Unique genomic coordinates Making up 7560 groups Consisting of 2261 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166114-chr5---16732014-16733752 l43 e 52 nr 1000000 chr ENSMUST00000033449-chrX---49321872-49324752 l43 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1011111 reads mapping to 313067 Unique genomic coordinates Making up 8197 groups Consisting of 2487 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000002495-chr7-+-16768640-16771853 l43 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 629613 reads mapping to 306091 Unique genomic coordinates Making up 8021 groups Consisting of 2379 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000047622-chr6---32131288-32133254 l43 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 616343 reads mapping to 310369 Unique genomic coordinates Making up 8148 groups Consisting of 2400 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000049714-chr11-+-83832362-83833955 l44 e 55 nr 1000000 chr ENSMUST00000066439-chr19-+-37663841-37665955 l44 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1272980 reads mapping to 290752 Unique genomic coordinates Making up 7655 groups Consisting of 2200 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000006587-chr2---167486373-167487056 l45 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 950084 reads mapping to 305070 Unique genomic coordinates Making up 7899 groups Consisting of 2391 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135776-chr5-+-106157242-106163257 l45 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 625921 reads mapping to 310376 Unique genomic coordinates Making up 8274 groups Consisting of 2520 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000119339-chr5-+-87244154-87246858 l43 e 58 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 679921 reads mapping to 287849 Unique genomic coordinates Making up 7502 groups Consisting of 2249 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000032192-chr6-+-108318505-108319659 l45 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 999817 reads mapping to 293132 Unique genomic coordinates Making up 7801 groups Consisting of 2347 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000115251-chr6---29492763-29493860 l43 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 718550 reads mapping to 293061 Unique genomic coordinates Making up 7649 groups Consisting of 2355 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030296-chr4-+-108507206-108507961 l45 e 61 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 649688 reads mapping to 294655 Unique genomic coordinates Making up 7672 groups Consisting of 2341 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022875-chr15-+-27482944-27484062 l44 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 969909 reads mapping to 302607 Unique genomic coordinates Making up 7872 groups Consisting of 2260 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000127456-chr4---58661264-58663463 l43 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 784675 reads mapping to 291404 Unique genomic coordinates Making up 7665 groups Consisting of 2243 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138273-chr6-+-14937823-14938964 l43 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 849122 reads mapping to 304682 Unique genomic coordinates Making up 8009 groups Consisting of 2366 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030257-chr4-+-100646111-100648065 l45 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 737292 reads mapping to 290652 Unique genomic coordinates Making up 7562 groups Consisting of 2212 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 476064 reads mapping to 264815 Unique genomic coordinates Making up 7020 groups Consisting of 2006 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000066160-chr5-+-111269036-111269567 l45 e 67 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 623678 reads mapping to 299799 Unique genomic coordinates Making up 7887 groups Consisting of 2347 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167896-chr4-+-155144078-155145068 l45 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 707946 reads mapping to 306813 Unique genomic coordinates Making up 8083 groups Consisting of 2355 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000013633-chr5-+-109133186-109135969 l45 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 786075 reads mapping to 284085 Unique genomic coordinates Making up 7517 groups Consisting of 2133 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000052826-chr7---110902664-110904670 l45 e 70 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 598158 reads mapping to 278163 Unique genomic coordinates Making up 7435 groups Consisting of 2236 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030489-chr4-+-114731624-114732771 l45 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 676552 reads mapping to 294920 Unique genomic coordinates Making up 7838 groups Consisting of 2296 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000137884-chr4-+-49218760-49221472 l43 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 857787 reads mapping to 306910 Unique genomic coordinates Making up 7989 groups Consisting of 2470 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000075159-chr5---76731949-76733573 l43 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 636327 reads mapping to 297201 Unique genomic coordinates Making up 7828 groups Consisting of 2321 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000101376-chr5-+-32634664-32636374 l43 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 918947 reads mapping to 303486 Unique genomic coordinates Making up 7950 groups Consisting of 2329 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000075806-chr16---29260503-29261575 l44 e 75 nr 1000000 chr ENSMUST00000075806-chr16---29260503-29261575 l44 e 75 nr 1500000 chr ENSMUST00000035014-chr9---115993415-116000175 l45 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1522695 reads mapping to 298995 Unique genomic coordinates Making up 7913 groups Consisting of 2352 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 ENSMUST00000148538-chr7-+-74148726-74149876 l43 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1635569 reads mapping to 289407 Unique genomic coordinates Making up 7560 groups Consisting of 2206 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000127296-chr9-+-22597695-22598877 l43 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 637163 reads mapping to 292172 Unique genomic coordinates Making up 7682 groups Consisting of 2281 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000097504-chr18---82779497-82780578 l44 e 78 nr 1000000 chr ENSMUST00000080744-chr4-+-111198689-111199778 l45 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1232684 reads mapping to 323623 Unique genomic coordinates Making up 8411 groups Consisting of 2566 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000146982-chr4-+-117659552-117660579 l45 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 659907 reads mapping to 293335 Unique genomic coordinates Making up 7807 groups Consisting of 2261 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000063975-chr2-+-118605455-118606180 l45 e 80 nr 1000000 chr ENSMUST00000118894-chrX-+-71978698-71979480 l43 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1008782 reads mapping to 308662 Unique genomic coordinates Making up 8045 groups Consisting of 2440 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 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 844856 reads mapping to 287185 Unique genomic coordinates Making up 7602 groups Consisting of 2232 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144066-chr2-+-145954190-145955482 l45 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 739316 reads mapping to 307538 Unique genomic coordinates Making up 8084 groups Consisting of 2432 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030112-chr4-+-40124312-40125483 l43 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 693127 reads mapping to 309054 Unique genomic coordinates Making up 8085 groups Consisting of 2421 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000171098-chr6---134191377-134192484 l45 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 583201 reads mapping to 282458 Unique genomic coordinates Making up 7492 groups Consisting of 2154 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000092167-chr10-+-115753922-115755185 l46 e 85 nr 1000000 chr ENSMUST00000144637-chr4---99368404-99369485 l43 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1304768 reads mapping to 306989 Unique genomic coordinates Making up 7952 groups Consisting of 2414 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138303-chr2---134995309-134997286 l45 e 86 nr 1000000 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 1266099 reads mapping to 308166 Unique genomic coordinates Making up 8088 groups Consisting of 2429 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035982-chr4---19576763-19578087 l43 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 781825 reads mapping to 312380 Unique genomic coordinates Making up 8212 groups Consisting of 2411 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000070720-chr5---36739715-36740788 l43 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 696190 reads mapping to 299397 Unique genomic coordinates Making up 7804 groups Consisting of 2306 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148563-chr6-+-121823133-121826989 l45 e 89 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 581852 reads mapping to 283228 Unique genomic coordinates Making up 7352 groups Consisting of 2270 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000110387-chr2---126959085-126959690 l45 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 815140 reads mapping to 291262 Unique genomic coordinates Making up 7575 groups Consisting of 2276 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000066849-chr3-+-130906674-130908391 l45 e 91 nr 1000000 chr ENSMUST00000070863-chr9-+-74800691-74803491 l43 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1044245 reads mapping to 303320 Unique genomic coordinates Making up 8111 groups Consisting of 2321 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000120437-chr2---173809983-173810192 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 ENSMUST00000032180-chr6---91358166-91359392 l43 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 3136850 reads mapping to 292482 Unique genomic coordinates Making up 7649 groups Consisting of 2260 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000172521-chr3---142491345-142492793 l45 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 734307 reads mapping to 309909 Unique genomic coordinates Making up 8128 groups Consisting of 2473 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000049454-chr7-+-19679893-19683694 l43 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 687519 reads mapping to 315246 Unique genomic coordinates Making up 8188 groups Consisting of 2390 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121469-chr6-+-71657555-71658495 l43 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 606334 reads mapping to 289285 Unique genomic coordinates Making up 7570 groups Consisting of 2266 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106176-chr4-+-124697351-124698496 l45 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 757205 reads mapping to 308501 Unique genomic coordinates Making up 8156 groups Consisting of 2515 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000047119-chr5---24259452-24260597 l43 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 756768 reads mapping to 292390 Unique genomic coordinates Making up 7554 groups Consisting of 2347 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170918-chr3---129006133-129007198 l45 e 98 nr 1000000 chr ENSMUST00000014421-chr5---90691784-90695098 l43 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1266319 reads mapping to 304393 Unique genomic coordinates Making up 7756 groups Consisting of 2370 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000151196-chr5---145844292-145844899 l45 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 684826 reads mapping to 292800 Unique genomic coordinates Making up 7652 groups Consisting of 2186 clusters