Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144159-chr13---24233600-24234100 l44 e 0 nr 1000000 chr ENSMUST00000142996-chr5-+-46033900-46034400 l43 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1306593 reads mapping to 472769 Unique genomic coordinates Making up 12637 groups Consisting of 4936 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169481-chr17---6369201-6369701 l42 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 929063 reads mapping to 467187 Unique genomic coordinates Making up 12701 groups Consisting of 4840 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109289-chr15---90806402-90806902 l44 e 2 nr 1000000 chr ENSMUST00000143085-chr7-+-3604302-3604802 l41 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1166410 reads mapping to 503149 Unique genomic coordinates Making up 13456 groups Consisting of 5174 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025462-chr18---80394101-80394403 l44 e 3 nr 1000000 chr ENSMUST00000035202-chr9-+-107800503-107801003 l45 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1034824 reads mapping to 468790 Unique genomic coordinates Making up 12517 groups Consisting of 4818 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024882-chr17-+-75239804-75240304 l44 e 4 nr 1000000 chr ENSMUST00000152878-chr9-+-7578238-7578904 l41 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1129723 reads mapping to 493000 Unique genomic coordinates Making up 13483 groups Consisting of 5214 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099653-chr16-+-59460705-59461205 l44 e 5 nr 1000000 chr ENSMUST00000072093-chr9-+-109007922-109008105 l45 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1031439 reads mapping to 495469 Unique genomic coordinates Making up 13411 groups Consisting of 5077 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000168690-chr15---10414606-10415106 l44 e 6 nr 1000000 chr ENSMUST00000135215-chr5-+-106314706-106315206 l45 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1228752 reads mapping to 482946 Unique genomic coordinates Making up 12984 groups Consisting of 4924 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000164268-chr19-+-45011577-45011807 l44 e 7 nr 1000000 chr ENSMUST00000112376-chrX-+-156986607-156987107 l45 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1002508 reads mapping to 483055 Unique genomic coordinates Making up 12846 groups Consisting of 4922 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114357-chr16---58486008-58486508 l44 e 8 nr 1000000 chr ENSMUST00000153686-chr7---133944508-133945008 l45 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1136779 reads mapping to 496943 Unique genomic coordinates Making up 13124 groups Consisting of 5163 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000172922-chr17-+-33674272-33675209 l44 e 9 nr 1000000 chr ENSMUST00000049251-chr6-+-30534509-30535009 l43 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1167954 reads mapping to 488135 Unique genomic coordinates Making up 13260 groups Consisting of 5031 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000037615-chr13---25018910-25019410 l44 e 10 nr 1000000 chr ENSMUST00000144822-chr2---90893510-90894010 l43 e 10 nr 1500000 chr ENSMUST00000035164-chr9-+-103240010-103240510 l45 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1547305 reads mapping to 505844 Unique genomic coordinates Making up 13539 groups Consisting of 5352 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091436-chr2---13277327-13278211 l43 e 11 nr 1000000 chr ENSMUST00000123530-chr9---103190011-103190511 l45 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1025038 reads mapping to 487328 Unique genomic coordinates Making up 13231 groups Consisting of 5172 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023600-chr16-+-72993412-72993912 l44 e 12 nr 1000000 chr ENSMUST00000075591-chr6---118544212-118544712 l45 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1218025 reads mapping to 513481 Unique genomic coordinates Making up 13795 groups Consisting of 5337 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000141222-chr2-+-3772413-3772913 l41 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 998089 reads mapping to 488584 Unique genomic coordinates Making up 13064 groups Consisting of 5050 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000090339-chr15---10518514-10519014 l44 e 14 nr 1000000 chr ENSMUST00000107178-chr4-+-85895814-85896314 l43 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1385996 reads mapping to 490923 Unique genomic coordinates Making up 13089 groups Consisting of 5015 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000015146-chr15-+-65702215-65702715 l44 e 15 nr 1000000 chr ENSMUST00000124058-chr6---98903815-98904315 l43 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1221012 reads mapping to 475579 Unique genomic coordinates Making up 12603 groups Consisting of 4885 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000154150-chr16---13872616-13873116 l44 e 16 nr 1000000 chr ENSMUST00000159159-chr3-+-137949916-137950416 l45 e 16 nr 1500000 chr ENSMUST00000159159-chr3-+-137949916-137950416 l45 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1979089 reads mapping to 492405 Unique genomic coordinates Making up 12964 groups Consisting of 5103 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148215-chr17-+-31298433-31299017 l44 e 17 nr 1000000 chr ENSMUST00000151861-chr9---20448517-20449017 l43 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1063437 reads mapping to 482540 Unique genomic coordinates Making up 12987 groups Consisting of 5198 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121584-chr16---98050718-98051218 l44 e 18 nr 1000000 chr ENSMUST00000030311-chr4-+-94319118-94319618 l43 e 18 nr 1500000 chr ENSMUST00000091190-chrY---601652-602018 l39 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1500163 reads mapping to 482733 Unique genomic coordinates Making up 12865 groups Consisting of 4972 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000057610-chr17---49628380-49629319 l44 e 19 nr 1000000 chr ENSMUST00000034745-chr9-+-70134219-70134719 l43 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1054518 reads mapping to 498855 Unique genomic coordinates Making up 13337 groups Consisting of 5058 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000160243-chr16---23011620-23012120 l44 e 20 nr 1000000 chr ENSMUST00000093038-chr8-+-127069202-127069920 l45 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1067924 reads mapping to 477337 Unique genomic coordinates Making up 12863 groups Consisting of 4952 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142999-chr17---23328221-23328721 l44 e 21 nr 1000000 chr ENSMUST00000034879-chr9-+-56335498-56336421 l43 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1073886 reads mapping to 472741 Unique genomic coordinates Making up 12624 groups Consisting of 4938 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000153545-chr18-+-50263022-50263522 l44 e 22 nr 1000000 chr ENSMUST00000077775-chrX-+-45477902-45478522 l43 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1024673 reads mapping to 492961 Unique genomic coordinates Making up 13233 groups Consisting of 5055 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024916-chr17---89171423-89171923 l44 e 23 nr 1000000 chr ENSMUST00000149889-chr6-+-67016323-67016823 l43 e 23 nr 1500000 chr ENSMUST00000075578-chr8---126478475-126478623 l45 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1819995 reads mapping to 499537 Unique genomic coordinates Making up 13270 groups Consisting of 5208 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000129635-chr17-+-71588041-71588424 l44 e 24 nr 1000000 chr ENSMUST00000130817-chr6---142439124-142439624 l45 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1173385 reads mapping to 498777 Unique genomic coordinates Making up 13300 groups Consisting of 5240 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000146993-chr15-+-88842625-88843125 l44 e 25 nr 1000000 chr ENSMUST00000032172-chr6---89517725-89518225 l43 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1228701 reads mapping to 505230 Unique genomic coordinates Making up 13462 groups Consisting of 5234 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000137147-chr17-+-28295326-28295826 l44 e 26 nr 1000000 chr ENSMUST00000113980-chr6-+-82978526-82979026 l43 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1190750 reads mapping to 487017 Unique genomic coordinates Making up 13099 groups Consisting of 5078 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000067538-chr17---56558508-56558827 l44 e 27 nr 1000000 chr ENSMUST00000046929-chr7---128802627-128803127 l45 e 27 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1121254 reads mapping to 498131 Unique genomic coordinates Making up 13268 groups Consisting of 5148 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000004057-chr16---36049428-36049928 l44 e 28 nr 1000000 chr ENSMUST00000140455-chr6---88824028-88824528 l43 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1176382 reads mapping to 497178 Unique genomic coordinates Making up 13031 groups Consisting of 5023 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000002445-chr17-+-56824929-56825429 l44 e 29 nr 1000000 chr ENSMUST00000072767-chr9---42814029-42814529 l43 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1045549 reads mapping to 486197 Unique genomic coordinates Making up 12875 groups Consisting of 5090 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023583-chr16-+-22895430-22895930 l44 e 30 nr 1000000 chr ENSMUST00000099092-chr2-+-164819611-164820430 l45 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1422196 reads mapping to 500619 Unique genomic coordinates Making up 13453 groups Consisting of 5134 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000059844-chr17---46880231-46880731 l44 e 31 nr 1000000 chr ENSMUST00000028233-chr2---34894231-34894731 l43 e 31 nr 1500000 chr ENSMUST00000146034-chr2---60805531-60806031 l43 e 31 nr 2000000 chr ENSMUST00000072634-chr9---30979631-30980131 l43 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 2358773 reads mapping to 496930 Unique genomic coordinates Making up 13166 groups Consisting of 5102 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022576-chr14-+-75642232-75642732 l44 e 32 nr 1000000 chr ENSMUST00000126252-chr4-+-139938132-139938632 l45 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1244989 reads mapping to 495193 Unique genomic coordinates Making up 13311 groups Consisting of 5159 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000172153-chr15-+-66588933-66589433 l44 e 33 nr 1000000 chr ENSMUST00000147026-chr7-+-36240640-36241133 l43 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1120134 reads mapping to 477089 Unique genomic coordinates Making up 12861 groups Consisting of 4876 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000067538-chr17---56557168-56558134 l44 e 34 nr 1000000 chr ENSMUST00000026907-chr8---46393234-46393734 l43 e 34 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1102726 reads mapping to 491469 Unique genomic coordinates Making up 13157 groups Consisting of 5167 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000073418-chr15---76014535-76015035 l44 e 35 nr 1000000 chr ENSMUST00000031411-chr5---122018032-122018935 l45 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1263752 reads mapping to 481950 Unique genomic coordinates Making up 12882 groups Consisting of 4922 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025337-chr18---38053863-38054836 l44 e 36 nr 1000000 chr ENSMUST00000034227-chr8---97219436-97219936 l43 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1067262 reads mapping to 480777 Unique genomic coordinates Making up 13066 groups Consisting of 5002 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165339-chr12-+-66192037-66192537 l44 e 37 nr 1000000 chr ENSMUST00000108068-chr4---41154137-41154637 l43 e 37 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1354208 reads mapping to 491936 Unique genomic coordinates Making up 12956 groups Consisting of 5149 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000162413-chr16---22250438-22250938 l44 e 38 nr 1000000 chr ENSMUST00000037440-chr9---53304738-53305238 l43 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1049853 reads mapping to 484651 Unique genomic coordinates Making up 12908 groups Consisting of 4987 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000160501-chr14-+-17242539-17243039 l44 e 39 nr 1000000 chr ENSMUST00000055296-chr6-+-71904839-71905339 l43 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1279651 reads mapping to 500846 Unique genomic coordinates Making up 13435 groups Consisting of 5195 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173814-chr17-+-37095740-37096240 l44 e 40 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 995292 reads mapping to 487298 Unique genomic coordinates Making up 13129 groups Consisting of 5086 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000132397-chr17-+-47748641-47749141 l44 e 41 nr 1000000 chr ENSMUST00000113832-chrX---94534541-94535041 l43 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1018278 reads mapping to 500346 Unique genomic coordinates Making up 13510 groups Consisting of 5218 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000124373-chr13-+-37918842-37919342 l44 e 42 nr 1000000 chr ENSMUST00000113888-chr6---83456242-83456742 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1218003 reads mapping to 486436 Unique genomic coordinates Making up 13069 groups Consisting of 5055 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000000724-chr17-+-53772043-53772543 l44 e 43 nr 1000000 chr ENSMUST00000002099-chr9-+-44592543-44593043 l43 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1042812 reads mapping to 500256 Unique genomic coordinates Making up 13207 groups Consisting of 5130 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000143717-chr15---3973344-3973844 l42 e 44 nr 1000000 chr ENSMUST00000128027-chr5---124710178-124710944 l45 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1283829 reads mapping to 490621 Unique genomic coordinates Making up 13026 groups Consisting of 5157 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000063775-chr18-+-68266345-68266845 l44 e 45 nr 1000000 chr ENSMUST00000170846-chr9-+-74864345-74864845 l43 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1067884 reads mapping to 491807 Unique genomic coordinates Making up 13504 groups Consisting of 5138 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023433-chr16-+-57147346-57147846 l44 e 46 nr 1000000 chr ENSMUST00000054979-chr5-+-104270746-104271246 l45 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1246276 reads mapping to 492570 Unique genomic coordinates Making up 13295 groups Consisting of 5157 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000069293-chr1-+-46142547-46143047 l43 e 47 nr 1000000 chr ENSMUST00000020208-chr10-+-93562647-93563147 l44 e 47 nr 1500000 chr ENSMUST00000143704-chr4---6343147-6343647 l41 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1836422 reads mapping to 489870 Unique genomic coordinates Making up 13106 groups Consisting of 4942 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148960-chr17---71350948-71351448 l44 e 48 nr 1000000 chr ENSMUST00000150434-chrX---105953148-105953648 l45 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1008872 reads mapping to 492501 Unique genomic coordinates Making up 13154 groups Consisting of 5172 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167706-chr10---115930849-115931349 l46 e 49 nr 1000000 chr ENSMUST00000108248-chr11-+-79383949-79384449 l44 e 49 nr 1500000 chr ENSMUST00000116375-chr2-+-172201749-172202249 l45 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1882527 reads mapping to 492026 Unique genomic coordinates Making up 13088 groups Consisting of 5055 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159574-chr13-+-104900650-104901150 l46 e 50 nr 1000000 chr ENSMUST00000133155-chr5-+-106306250-106306750 l45 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1215649 reads mapping to 487389 Unique genomic coordinates Making up 13036 groups Consisting of 5036 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000042345-chr18-+-35403809-35404351 l44 e 51 nr 1000000 chr ENSMUST00000075245-chr9---73584551-73585051 l43 e 51 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1040314 reads mapping to 475920 Unique genomic coordinates Making up 12820 groups Consisting of 4927 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000082337-chr17-+-35985802-35985952 l44 e 52 nr 1000000 chr ENSMUST00000034466-chr8-+-127404252-127404752 l45 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1063970 reads mapping to 509256 Unique genomic coordinates Making up 13685 groups Consisting of 5400 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142213-chr18-+-32403953-32404453 l44 e 53 nr 1000000 chr ENSMUST00000163192-chr9---36591553-36592053 l43 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1069796 reads mapping to 487844 Unique genomic coordinates Making up 13085 groups Consisting of 5073 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036017-chr16-+-5081754-5082254 l42 e 54 nr 1000000 chr ENSMUST00000085754-chr9-+-55248454-55248954 l43 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1060128 reads mapping to 501611 Unique genomic coordinates Making up 13339 groups Consisting of 5307 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000001927-chr17-+-75651755-75652255 l44 e 55 nr 1000000 chr ENSMUST00000095424-chr8-+-22224292-22224855 l43 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1100596 reads mapping to 502010 Unique genomic coordinates Making up 13312 groups Consisting of 5247 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000004057-chr16---36071056-36071556 l44 e 56 nr 1000000 chr ENSMUST00000164568-chr7-+-88477256-88477756 l43 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1160253 reads mapping to 511955 Unique genomic coordinates Making up 13512 groups Consisting of 5261 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000065916-chr15-+-66517057-66517557 l44 e 57 nr 1000000 chr ENSMUST00000029485-chr3-+-108345519-108346357 l45 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1368767 reads mapping to 478249 Unique genomic coordinates Making up 12626 groups Consisting of 4977 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024852-chr17-+-71885909-71886558 l44 e 58 nr 1000000 chr ENSMUST00000053407-chr9-+-3369158-3369658 l41 e 58 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1063299 reads mapping to 490745 Unique genomic coordinates Making up 13088 groups Consisting of 5007 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025428-chr18---69104359-69104859 l44 e 59 nr 1000000 chr ENSMUST00000035369-chr8---116278559-116279059 l45 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1147537 reads mapping to 486582 Unique genomic coordinates Making up 12956 groups Consisting of 4981 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023336-chr16---46108660-46109160 l44 e 60 nr 1000000 chr ENSMUST00000162461-chr6-+-119866060-119866560 l45 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1197542 reads mapping to 484313 Unique genomic coordinates Making up 13015 groups Consisting of 5013 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000040518-chr15-+-78906761-78907261 l44 e 61 nr 1000000 chr ENSMUST00000086341-chr7-+-24206561-24207061 l43 e 61 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1149859 reads mapping to 504378 Unique genomic coordinates Making up 13136 groups Consisting of 5192 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000019723-chr17---56322662-56323162 l44 e 62 nr 1000000 chr ENSMUST00000073127-chr9-+-26896962-26897462 l43 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1081299 reads mapping to 494421 Unique genomic coordinates Making up 13329 groups Consisting of 5058 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148131-chr16---20711263-20711763 l44 e 63 nr 1000000 chr ENSMUST00000141532-chr5-+-110953563-110954063 l45 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1420659 reads mapping to 492940 Unique genomic coordinates Making up 13206 groups Consisting of 5032 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000072776-chr15---82236508-82237364 l44 e 64 nr 1000000 chr ENSMUST00000127253-chr7---107746964-107747464 l45 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1147447 reads mapping to 495192 Unique genomic coordinates Making up 13209 groups Consisting of 5063 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000041772-chr18-+-50091065-50091565 l44 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 990672 reads mapping to 481218 Unique genomic coordinates Making up 12944 groups Consisting of 5018 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170827-chr17-+-13989466-13989966 l44 e 66 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 974537 reads mapping to 470469 Unique genomic coordinates Making up 12691 groups Consisting of 4798 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000016144-chr13-+-113624567-113625067 l46 e 67 nr 1000000 chr ENSMUST00000029814-chr3-+-135169967-135170467 l45 e 67 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1283256 reads mapping to 483139 Unique genomic coordinates Making up 12929 groups Consisting of 5040 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000075856-chr19---4351830-4352268 l42 e 68 nr 1000000 chr ENSMUST00000034955-chr9-+-65329168-65329668 l43 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1048515 reads mapping to 501246 Unique genomic coordinates Making up 13479 groups Consisting of 5198 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000100655-chr15---57859669-57860169 l44 e 69 nr 1000000 chr ENSMUST00000164629-chr8-+-10013669-10014169 l43 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1079182 reads mapping to 475832 Unique genomic coordinates Making up 12945 groups Consisting of 4959 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000145726-chr18-+-50249470-50249970 l44 e 70 nr 1000000 chr ENSMUST00000037798-chr9---64774142-64774970 l43 e 70 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1054683 reads mapping to 474772 Unique genomic coordinates Making up 12592 groups Consisting of 4821 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023615-chr16---94725983-94726971 l44 e 71 nr 1000000 chr ENSMUST00000167004-chr8---24318271-24318771 l43 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1104228 reads mapping to 479597 Unique genomic coordinates Making up 12928 groups Consisting of 4898 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000072141-chr19-+-47168372-47168872 l44 e 72 nr 1000000 chr ENSMUST00000043784-chr4-+-46018572-46019072 l43 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1287456 reads mapping to 469832 Unique genomic coordinates Making up 12764 groups Consisting of 4973 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000171870-chr18---14129373-14129873 l44 e 73 nr 1000000 chr ENSMUST00000036606-chrX-+-96266837-96267773 l43 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1010581 reads mapping to 486440 Unique genomic coordinates Making up 13030 groups Consisting of 5035 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022640-chr14---69130174-69130674 l44 e 74 nr 1000000 chr ENSMUST00000102704-chr4---115782074-115782574 l45 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1345138 reads mapping to 501021 Unique genomic coordinates Making up 13451 groups Consisting of 5164 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000049872-chr14---122363775-122364275 l46 e 75 nr 1000000 chr ENSMUST00000124531-chr6---115772320-115773275 l45 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1181650 reads mapping to 481436 Unique genomic coordinates Making up 12952 groups Consisting of 4924 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169941-chr19---41163376-41163876 l44 e 76 nr 1000000 chr ENSMUST00000076889-chr9-+-75175076-75175576 l43 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1036784 reads mapping to 476581 Unique genomic coordinates Making up 12688 groups Consisting of 4931 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114076-chr16---91068777-91069277 l44 e 77 nr 1000000 chr ENSMUST00000033983-chr8---32273577-32274077 l43 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1088165 reads mapping to 493164 Unique genomic coordinates Making up 13199 groups Consisting of 5176 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000153613-chr17-+-89043178-89043678 l44 e 78 nr 1000000 chr ENSMUST00000169944-chr7---148512678-148513178 l45 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1188696 reads mapping to 513333 Unique genomic coordinates Making up 13658 groups Consisting of 5308 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000043211-chr10---127801562-127802079 l46 e 79 nr 1000000 chr ENSMUST00000102694-chr3---100881379-100881879 l45 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1348765 reads mapping to 489415 Unique genomic coordinates Making up 13349 groups Consisting of 5135 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000087689-chr19-+-17252780-17253280 l44 e 80 nr 1000000 chr ENSMUST00000114030-chrX-+-75371474-75372380 l43 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1016112 reads mapping to 480084 Unique genomic coordinates Making up 13002 groups Consisting of 5011 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000011733-chr17-+-56134939-56135281 l44 e 81 nr 1000000 chr ENSMUST00000035850-chr9-+-53371781-53372281 l43 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1082954 reads mapping to 481656 Unique genomic coordinates Making up 12813 groups Consisting of 4826 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000168722-chr15-+-59368582-59369082 l44 e 82 nr 1000000 chr ENSMUST00000150755-chr4-+-108977445-108978282 l45 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1278706 reads mapping to 485592 Unique genomic coordinates Making up 12987 groups Consisting of 4977 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170156-chr13---11944883-11945383 l44 e 83 nr 1000000 chr ENSMUST00000169126-chr17---8019383-8019883 l42 e 83 nr 1500000 chr ENSMUST00000173287-chr7-+-89715583-89716083 l43 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1658593 reads mapping to 495830 Unique genomic coordinates Making up 13207 groups Consisting of 5112 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000097418-chr17-+-8444284-8444784 l42 e 84 nr 1000000 chr ENSMUST00000014562-chr7---54029684-54030184 l43 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1165678 reads mapping to 486028 Unique genomic coordinates Making up 13178 groups Consisting of 4949 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024879-chr17-+-75091685-75092185 l44 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 991482 reads mapping to 478316 Unique genomic coordinates Making up 12812 groups Consisting of 4995 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159775-chr15-+-57750986-57751486 l44 e 86 nr 1000000 chr ENSMUST00000118133-chr6-+-15203786-15204286 l43 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1482030 reads mapping to 504530 Unique genomic coordinates Making up 13558 groups Consisting of 5204 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000048188-chr15-+-66459987-66460487 l44 e 87 nr 1000000 chr ENSMUST00000033198-chr7---127334087-127334587 l45 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1110344 reads mapping to 501636 Unique genomic coordinates Making up 13364 groups Consisting of 5157 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091863-chr18-+-68019688-68020188 l44 e 88 nr 1000000 chr ENSMUST00000112334-chrX---158909788-158910288 l45 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1001043 reads mapping to 503218 Unique genomic coordinates Making up 13521 groups Consisting of 5244 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091436-chr2---13283989-13284489 l43 e 89 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 972219 reads mapping to 483803 Unique genomic coordinates Making up 12952 groups Consisting of 5013 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000068756-chr15---73036690-73037190 l44 e 90 nr 1000000 chr ENSMUST00000116615-chr9---31719990-31720490 l43 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1052800 reads mapping to 484837 Unique genomic coordinates Making up 12982 groups Consisting of 5179 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121927-chr16---76352791-76353291 l44 e 91 nr 1000000 chr ENSMUST00000146115-chr5---8978291-8978791 l41 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1253630 reads mapping to 505776 Unique genomic coordinates Making up 13484 groups Consisting of 5279 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000050664-chr13-+-13822092-13822592 l44 e 92 nr 1000000 chr ENSMUST00000113493-chr5-+-76969792-76970292 l43 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1290014 reads mapping to 483532 Unique genomic coordinates Making up 12893 groups Consisting of 5074 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022574-chr14---75484793-75485293 l44 e 93 nr 1000000 chr ENSMUST00000147729-chr5-+-100956493-100956993 l45 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1263518 reads mapping to 494583 Unique genomic coordinates Making up 13286 groups Consisting of 5179 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000060103-chr17---15059385-15060094 l44 e 94 nr 1000000 chr ENSMUST00000137373-chr7-+-20403294-20403794 l43 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1206931 reads mapping to 518770 Unique genomic coordinates Making up 13912 groups Consisting of 5469 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161283-chr19-+-11596295-11596795 l44 e 95 nr 1000000 chr ENSMUST00000148135-chrX---7705340-7706095 l41 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1036638 reads mapping to 496788 Unique genomic coordinates Making up 13265 groups Consisting of 5098 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000069345-chr16-+-33946696-33947196 l44 e 96 nr 1000000 chr ENSMUST00000140466-chr9---6955996-6956496 l41 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1109761 reads mapping to 486797 Unique genomic coordinates Making up 12963 groups Consisting of 5017 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000168680-chr16-+-49068997-49069497 l44 e 97 nr 1000000 chr ENSMUST00000006956-chr7---53968097-53968597 l43 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1151159 reads mapping to 497346 Unique genomic coordinates Making up 13196 groups Consisting of 5192 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025217-chr18---35105098-35105598 l44 e 98 nr 1000000 chr ENSMUST00000025217-chr18---35105098-35105598 l44 e 98 nr 1500000 chr ENSMUST00000034239-chr8-+-97605998-97606498 l43 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1609360 reads mapping to 502343 Unique genomic coordinates Making up 13512 groups Consisting of 5262 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000047168-chr17-+-31608799-31609299 l44 e 99 nr 1000000 chr ENSMUST00000122087-chr9-+-69862298-69863099 l43 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1052991 reads mapping to 484008 Unique genomic coordinates Making up 12962 groups Consisting of 5080 clusters