Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159983-chr19---7671150-7673900 l42 e 0 nr 1000000 chr ENSMUST00000162538-chr8---97355173-97357100 l43 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1081750 reads mapping to 471072 Unique genomic coordinates Making up 13091 groups Consisting of 4310 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166793-chr18-+-35740324-35743001 l44 e 1 nr 1000000 chr ENSMUST00000132097-chr9-+-28872891-28874901 l43 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1051030 reads mapping to 481278 Unique genomic coordinates Making up 13405 groups Consisting of 4309 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036972-chr14---50389554-50390802 l44 e 2 nr 1000000 chr ENSMUST00000111845-chr6-+-140598777-140604002 l45 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1348312 reads mapping to 521867 Unique genomic coordinates Making up 14574 groups Consisting of 4817 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026008-chr19-+-46576138-46578003 l44 e 3 nr 1000000 chr ENSMUST00000093599-chr6---3671897-3672003 l41 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1324510 reads mapping to 489130 Unique genomic coordinates Making up 13547 groups Consisting of 4417 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025129-chr18---7439067-7441004 l42 e 4 nr 1000000 chr ENSMUST00000091146-chr2-+-29579793-29580904 l43 e 4 nr 1500000 chr ENSMUST00000165064-chr5-+-33702501-33703704 l43 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1804132 reads mapping to 516283 Unique genomic coordinates Making up 14294 groups Consisting of 4659 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000080297-chr16---4087181-4088905 l42 e 5 nr 1000000 chr ENSMUST00000172269-chr7---28232057-28232705 l43 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1142561 reads mapping to 515390 Unique genomic coordinates Making up 14436 groups Consisting of 4644 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000130623-chr17-+-45059628-45062806 l44 e 6 nr 1000000 chr ENSMUST00000095323-chr8---47058358-47060606 l43 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1155299 reads mapping to 490894 Unique genomic coordinates Making up 13541 groups Consisting of 4371 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000168985-chr14---87406482-87407707 l44 e 7 nr 1000000 chr ENSMUST00000118133-chr6-+-15203786-15205007 l43 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1211851 reads mapping to 505610 Unique genomic coordinates Making up 14078 groups Consisting of 4611 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000072685-chr19---50242509-50243608 l44 e 8 nr 1000000 chr ENSMUST00000138918-chrX---148771395-148772608 l45 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1008059 reads mapping to 485656 Unique genomic coordinates Making up 13414 groups Consisting of 4327 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000089398-chr15---78320112-78322809 l44 e 9 nr 1000000 chr ENSMUST00000166521-chr6-+-87845188-87846609 l43 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1175538 reads mapping to 484346 Unique genomic coordinates Making up 13533 groups Consisting of 4514 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000069245-chr18-+-44166783-44167910 l44 e 10 nr 1000000 chr ENSMUST00000033999-chr8---42483810-42485510 l43 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1089454 reads mapping to 483639 Unique genomic coordinates Making up 13456 groups Consisting of 4472 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000009877-chr15---100347881-100349611 l46 e 11 nr 1000000 chr ENSMUST00000154893-chr7---73486556-73488311 l43 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1181832 reads mapping to 488618 Unique genomic coordinates Making up 13476 groups Consisting of 4448 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022585-chr14---76494314-76495412 l44 e 12 nr 1000000 chr ENSMUST00000143457-chr4-+-155227027-155233412 l45 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1286734 reads mapping to 503870 Unique genomic coordinates Making up 14005 groups Consisting of 4535 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000001147-chr10---76187184-76188913 l44 e 13 nr 1000000 chr ENSMUST00000164115-chr12-+-73597536-73599413 l44 e 13 nr 1500000 chr ENSMUST00000164115-chr12-+-73597536-73599413 l44 e 13 nr 2000000 chr ENSMUST00000167724-chr19-+-36939942-36941113 l44 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 2440137 reads mapping to 511445 Unique genomic coordinates Making up 14041 groups Consisting of 4688 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169862-chr18-+-14979447-14981214 l44 e 14 nr 1000000 chr ENSMUST00000137822-chr8---13575837-13579214 l43 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1386657 reads mapping to 509889 Unique genomic coordinates Making up 14244 groups Consisting of 4686 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000079642-chr17---56004469-56006415 l44 e 15 nr 1000000 chr ENSMUST00000035208-chr9---108091875-108092715 l45 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1025812 reads mapping to 507086 Unique genomic coordinates Making up 14262 groups Consisting of 4641 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000088811-chr17-+-21161925-21165816 l44 e 16 nr 1000000 chr ENSMUST00000112387-chr9-+-107479258-107482216 l45 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1032340 reads mapping to 489881 Unique genomic coordinates Making up 13645 groups Consisting of 4400 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170858-chr17-+-12407642-12408717 l44 e 17 nr 1000000 chr ENSMUST00000118395-chr8---125825975-125833017 l45 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1099707 reads mapping to 514454 Unique genomic coordinates Making up 14362 groups Consisting of 4698 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000124324-chr15---100229345-100230418 l46 e 18 nr 1000000 chr ENSMUST00000106157-chr7-+-140140768-140142618 l45 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1124517 reads mapping to 496331 Unique genomic coordinates Making up 13805 groups Consisting of 4509 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000124845-chr15-+-80836334-80842719 l44 e 19 nr 1000000 chr ENSMUST00000116456-chr5-+-144467453-144471119 l45 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1213681 reads mapping to 526522 Unique genomic coordinates Making up 14575 groups Consisting of 4790 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000061052-chr17---36045008-36047020 l44 e 20 nr 1000000 chr ENSMUST00000034561-chr9-+-50630190-50631320 l43 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1062446 reads mapping to 475279 Unique genomic coordinates Making up 13317 groups Consisting of 4274 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025485-chr18-+-65080790-65081421 l44 e 21 nr 1000000 chr ENSMUST00000163624-chr9---63383542-63384621 l43 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1041423 reads mapping to 462492 Unique genomic coordinates Making up 13027 groups Consisting of 4265 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023611-chr16---85858415-85863922 l44 e 22 nr 1000000 chr ENSMUST00000014990-chr8---107994680-107995322 l45 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1139973 reads mapping to 499771 Unique genomic coordinates Making up 13944 groups Consisting of 4652 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024553-chr16---32084504-32085923 l44 e 23 nr 1000000 chr ENSMUST00000068485-chr7-+-103106725-103110123 l45 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1139946 reads mapping to 506669 Unique genomic coordinates Making up 14105 groups Consisting of 4612 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000120266-chr13-+-33599996-33600624 l44 e 24 nr 1000000 chr ENSMUST00000044564-chr4-+-119298394-119301724 l45 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1371802 reads mapping to 523213 Unique genomic coordinates Making up 14546 groups Consisting of 4782 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138333-chr11---82009749-82011325 l44 e 25 nr 1000000 chr ENSMUST00000153809-chr4-+-132258847-132260825 l45 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1343811 reads mapping to 490267 Unique genomic coordinates Making up 13659 groups Consisting of 4482 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000101435-chr12-+-53644683-53646626 l44 e 26 nr 1000000 chr ENSMUST00000154682-chr2---29106430-29108526 l43 e 26 nr 1500000 chr ENSMUST00000034150-chr8---83297949-83299426 l43 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1618004 reads mapping to 530722 Unique genomic coordinates Making up 14565 groups Consisting of 4793 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024826-chr17---31277994-31281227 l44 e 27 nr 1000000 chr ENSMUST00000134056-chr7---150901071-150902227 l45 e 27 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1130982 reads mapping to 484219 Unique genomic coordinates Making up 13370 groups Consisting of 4423 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000128199-chr2-+-28302320-28304928 l43 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 936083 reads mapping to 486747 Unique genomic coordinates Making up 13701 groups Consisting of 4367 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142066-chr18---12463620-12464229 l44 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 974039 reads mapping to 482782 Unique genomic coordinates Making up 13460 groups Consisting of 4289 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000067048-chr15-+-28312831-28314730 l44 e 30 nr 1000000 chr ENSMUST00000095922-chr5---109514868-109516230 l45 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1230613 reads mapping to 517619 Unique genomic coordinates Making up 14543 groups Consisting of 4760 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000053336-chr16---21649118-21654331 l44 e 31 nr 1000000 chr ENSMUST00000126774-chr6-+-146948963-146950031 l45 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1272155 reads mapping to 511161 Unique genomic coordinates Making up 14248 groups Consisting of 4716 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000130579-chr18---84803444-84804532 l44 e 32 nr 1000000 chr ENSMUST00000119291-chr9-+-115845760-115846932 l45 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1029506 reads mapping to 491288 Unique genomic coordinates Making up 13732 groups Consisting of 4469 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165610-chr11---79295221-79297533 l44 e 33 nr 1000000 chr ENSMUST00000028630-chr2-+-125031251-125032333 l45 e 33 nr 1500000 chr ENSMUST00000070617-chr9---119728347-119729633 l45 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1598046 reads mapping to 502707 Unique genomic coordinates Making up 14029 groups Consisting of 4504 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000155032-chr11-+-41617357-41618434 l44 e 34 nr 1000000 chr ENSMUST00000171739-chr3---81763892-81765934 l43 e 34 nr 1500000 chr ENSMUST00000031536-chr5---140803628-140805234 l45 e 34 nr 2000000 chr ENSMUST00000031536-chr5---140803628-140805234 l45 e 34 nr 2500000 chr ENSMUST00000031536-chr5---140803628-140805234 l45 e 34 nr 3000000 chr ENSMUST00000031536-chr5---140803628-140805234 l45 e 34 nr 3500000 chr ENSMUST00000050561-chr8---72549227-72553634 l43 e 34 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 3594018 reads mapping to 490927 Unique genomic coordinates Making up 13687 groups Consisting of 4576 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000075317-chr15---12300844-12306635 l44 e 35 nr 1000000 chr ENSMUST00000142822-chr8---67560289-67561235 l43 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1112410 reads mapping to 505696 Unique genomic coordinates Making up 14169 groups Consisting of 4626 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036937-chr15-+-58704204-58708336 l44 e 36 nr 1000000 chr ENSMUST00000100947-chr5---108244130-108246436 l45 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1229795 reads mapping to 498015 Unique genomic coordinates Making up 13768 groups Consisting of 4594 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000036690-chr11-+-121702325-121704737 l46 e 37 nr 1000000 chr ENSMUST00000029574-chr3---115816771-115818037 l45 e 37 nr 1500000 chr ENSMUST00000065112-chr9---30728366-30730037 l43 e 37 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1616348 reads mapping to 489033 Unique genomic coordinates Making up 13506 groups Consisting of 4495 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165110-chr17-+-12511751-12512538 l44 e 38 nr 1000000 chr ENSMUST00000134646-chr7-+-72752531-72756638 l43 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1152168 reads mapping to 481657 Unique genomic coordinates Making up 13315 groups Consisting of 4455 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144922-chr11-+-66111721-66114739 l44 e 39 nr 1000000 chr ENSMUST00000144922-chr11-+-66111721-66114739 l44 e 39 nr 1500000 chr ENSMUST00000015227-chr2---25356548-25357239 l43 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1936189 reads mapping to 507892 Unique genomic coordinates Making up 14136 groups Consisting of 4687 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000046663-chr16-+-58463803-58469840 l44 e 40 nr 1000000 chr ENSMUST00000146828-chr6-+-47444566-47445740 l43 e 40 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1210145 reads mapping to 489926 Unique genomic coordinates Making up 13621 groups Consisting of 4520 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023696-chr16---90936346-90941241 l44 e 41 nr 1000000 chr ENSMUST00000075588-chr7---150820713-150824841 l45 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1116194 reads mapping to 521956 Unique genomic coordinates Making up 14648 groups Consisting of 4715 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000076431-chr2-+-26250045-26252642 l43 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 922686 reads mapping to 477451 Unique genomic coordinates Making up 13366 groups Consisting of 4500 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000088420-chr17---24732882-24740743 l44 e 43 nr 1000000 chr ENSMUST00000068071-chr9-+-110214573-110215643 l45 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1047277 reads mapping to 511542 Unique genomic coordinates Making up 14245 groups Consisting of 4713 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000064405-chr16---63584283-63585344 l44 e 44 nr 1000000 chr ENSMUST00000148739-chr6---145313654-145315844 l45 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1149381 reads mapping to 498717 Unique genomic coordinates Making up 13754 groups Consisting of 4606 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000109735-chr13---67413934-67416345 l44 e 45 nr 1000000 chr ENSMUST00000025850-chr19-+-5453913-5455945 l42 e 45 nr 1500000 chr ENSMUST00000170413-chrX-+-126505315-126507645 l45 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1580828 reads mapping to 509438 Unique genomic coordinates Making up 14177 groups Consisting of 4616 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000092723-chr17-+-5338716-5339846 l42 e 46 nr 1000000 chr ENSMUST00000126443-chr7-+-36557397-36559646 l43 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1203492 reads mapping to 523093 Unique genomic coordinates Making up 14454 groups Consisting of 4811 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000075510-chr17---56702362-56707547 l44 e 47 nr 1000000 chr ENSMUST00000108569-chr7---5364103-5364747 l41 e 47 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1153235 reads mapping to 482487 Unique genomic coordinates Making up 13434 groups Consisting of 4369 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000087031-chr17-+-46374822-46379248 l44 e 48 nr 1000000 chr ENSMUST00000066875-chr8-+-109027676-109028948 l45 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1220152 reads mapping to 489818 Unique genomic coordinates Making up 13510 groups Consisting of 4451 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000053754-chr19---5453163-5457549 l42 e 49 nr 1000000 chr ENSMUST00000172988-chr7-+-63023548-63025249 l43 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1132920 reads mapping to 506667 Unique genomic coordinates Making up 14138 groups Consisting of 4593 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000045173-chr13-+-56730479-56734850 l44 e 50 nr 1000000 chr ENSMUST00000111430-chr2-+-90958301-90966950 l43 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1453344 reads mapping to 506315 Unique genomic coordinates Making up 14090 groups Consisting of 4680 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000005365-chr2---69042413-69044251 l43 e 51 nr 1000000 chr ENSMUST00000026029-chrX-+-150916545-150917651 l45 e 51 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1058286 reads mapping to 472652 Unique genomic coordinates Making up 13137 groups Consisting of 4370 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023828-chr18-+-89214908-89216052 l44 e 52 nr 1000000 chr ENSMUST00000123926-chr9---107500005-107507852 l45 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1050668 reads mapping to 508788 Unique genomic coordinates Making up 14321 groups Consisting of 4687 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121524-chr13-+-21995025-21996653 l44 e 53 nr 1000000 chr ENSMUST00000031092-chr5---65669450-65671553 l43 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1265980 reads mapping to 516335 Unique genomic coordinates Making up 14335 groups Consisting of 4721 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000024896-chr17---65183112-65184454 l44 e 54 nr 1000000 chr ENSMUST00000108745-chr8-+-131608571-131609654 l45 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1094108 reads mapping to 509259 Unique genomic coordinates Making up 14284 groups Consisting of 4627 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000174195-chr17---37002750-37004155 l44 e 55 nr 1000000 chr ENSMUST00000026897-chr7---81426744-81430055 l43 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1175341 reads mapping to 483227 Unique genomic coordinates Making up 13688 groups Consisting of 4430 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166231-chr15-+-44715020-44715856 l44 e 56 nr 1000000 chr ENSMUST00000028336-chr2-+-53051122-53052056 l43 e 56 nr 1500000 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 1594257 reads mapping to 506471 Unique genomic coordinates Making up 14024 groups Consisting of 4733 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165541-chr15-+-73581059-73582957 l44 e 57 nr 1000000 chr ENSMUST00000030443-chr4-+-116780004-116784757 l45 e 57 nr 1500000 chr ENSMUST00000114354-chrX---71264739-71269257 l43 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1667220 reads mapping to 513511 Unique genomic coordinates Making up 14111 groups Consisting of 4700 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000061856-chr19---55148561-55151358 l44 e 58 nr 1000000 chr ENSMUST00000034607-chr9---44557908-44560858 l43 e 58 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1064328 reads mapping to 483523 Unique genomic coordinates Making up 13442 groups Consisting of 4521 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000079009-chr12-+-113262373-113265859 l46 e 59 nr 1000000 chr ENSMUST00000143245-chr5-+-100506981-100507659 l45 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1250634 reads mapping to 482312 Unique genomic coordinates Making up 13409 groups Consisting of 4452 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136840-chr15-+-76541053-76542460 l44 e 60 nr 1000000 chr ENSMUST00000150829-chr5-+-76964079-76968760 l43 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1301428 reads mapping to 484352 Unique genomic coordinates Making up 13384 groups Consisting of 4416 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023393-chr16-+-70568734-70569961 l44 e 61 nr 1000000 chr ENSMUST00000047173-chr9-+-4383037-4386861 l41 e 61 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1091114 reads mapping to 497677 Unique genomic coordinates Making up 13638 groups Consisting of 4652 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000097381-chr17-+-22741535-22742762 l44 e 62 nr 1000000 chr ENSMUST00000142260-chr7---52824456-52827062 l43 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1148317 reads mapping to 507586 Unique genomic coordinates Making up 14237 groups Consisting of 4586 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025393-chr18---73808039-73810063 l44 e 63 nr 1000000 chr ENSMUST00000120347-chrX---110147802-110149263 l45 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1016765 reads mapping to 490444 Unique genomic coordinates Making up 13606 groups Consisting of 4354 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023210-chr15-+-76173953-76176364 l44 e 64 nr 1000000 chr ENSMUST00000166898-chr4---41941480-41943464 l43 e 64 nr 1500000 chr ENSMUST00000054594-chr7-+-31099835-31104064 l43 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1776125 reads mapping to 516021 Unique genomic coordinates Making up 14429 groups Consisting of 4759 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142025-chr19-+-9352520-9353665 l42 e 65 nr 1000000 chr ENSMUST00000089060-chrX---35393964-35395465 l43 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1028828 reads mapping to 491988 Unique genomic coordinates Making up 13620 groups Consisting of 4509 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114251-chr2---25322229-25325566 l43 e 66 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 939638 reads mapping to 445978 Unique genomic coordinates Making up 12508 groups Consisting of 4168 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 988652 reads mapping to 490417 Unique genomic coordinates Making up 13805 groups Consisting of 4558 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000114371-chr16---57310866-57311968 l44 e 68 nr 1000000 chr ENSMUST00000140956-chr3---37207544-37211368 l43 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1369534 reads mapping to 513637 Unique genomic coordinates Making up 14368 groups Consisting of 4641 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023019-chr15-+-85722497-85723669 l44 e 69 nr 1000000 chr ENSMUST00000155415-chr6-+-146960477-146961969 l45 e 69 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1161030 reads mapping to 491035 Unique genomic coordinates Making up 13455 groups Consisting of 4381 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000015719-chr17-+-26819123-26820170 l44 e 70 nr 1000000 chr ENSMUST00000034717-chr9---21571217-21575070 l43 e 70 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1052215 reads mapping to 478776 Unique genomic coordinates Making up 13316 groups Consisting of 4429 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167795-chr18---42384908-42385971 l44 e 71 nr 1000000 chr ENSMUST00000149260-chrX-+-143421026-143423871 l45 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1005840 reads mapping to 493152 Unique genomic coordinates Making up 13597 groups Consisting of 4532 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000106227-chr11---119931103-119935672 l46 e 72 nr 1000000 chr ENSMUST00000030158-chr4---41661830-41664972 l43 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1408710 reads mapping to 510466 Unique genomic coordinates Making up 14203 groups Consisting of 4736 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025521-chr18---61178516-61180673 l44 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 989976 reads mapping to 487458 Unique genomic coordinates Making up 13665 groups Consisting of 4438 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025681-chr19-+-6312719-6319074 l42 e 74 nr 1000000 chr ENSMUST00000008826-chrX-+-71516151-71518474 l43 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1022245 reads mapping to 498365 Unique genomic coordinates Making up 13970 groups Consisting of 4455 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173452-chr17-+-36644125-36644675 l44 e 75 nr 1000000 chr ENSMUST00000010208-chr9---107556854-107562075 l45 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1045633 reads mapping to 500222 Unique genomic coordinates Making up 14110 groups Consisting of 4633 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000162645-chr14-+-26472309-26476976 l44 e 76 nr 1000000 chr ENSMUST00000063813-chr5-+-32003699-32004976 l43 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1285201 reads mapping to 480947 Unique genomic coordinates Making up 13213 groups Consisting of 4425 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000069597-chr18-+-54076129-54077277 l44 e 77 nr 1000000 chr ENSMUST00000002025-chr8-+-69035639-69037677 l43 e 77 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1107240 reads mapping to 495239 Unique genomic coordinates Making up 13717 groups Consisting of 4523 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000047408-chr10---80692737-80693578 l44 e 78 nr 1000000 chr ENSMUST00000091420-chr2---17965710-17970678 l43 e 78 nr 1500000 chr ENSMUST00000118399-chrX---154237956-154239278 l45 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1503232 reads mapping to 531198 Unique genomic coordinates Making up 14732 groups Consisting of 4850 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135899-chr17-+-26919023-26922879 l44 e 79 nr 1000000 chr ENSMUST00000065545-chrY---65557-66679 l37 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1000484 reads mapping to 490476 Unique genomic coordinates Making up 13790 groups Consisting of 4520 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000082254-chr18---43696810-43697880 l44 e 80 nr 1000000 chr ENSMUST00000041761-chr7---96656295-96659880 l43 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1167739 reads mapping to 507379 Unique genomic coordinates Making up 14035 groups Consisting of 4699 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000091831-chr18-+-76461233-76462681 l44 e 81 nr 1000000 chr ENSMUST00000089295-chr6---96963866-96964981 l43 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1162827 reads mapping to 472260 Unique genomic coordinates Making up 13107 groups Consisting of 4332 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000141187-chr15-+-92075659-92079882 l44 e 82 nr 1000000 chr ENSMUST00000086763-chr17-+-57599616-57600682 l44 e 82 nr 1500000 chr ENSMUST00000108026-chr4-+-41836784-41842582 l43 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1956025 reads mapping to 510623 Unique genomic coordinates Making up 14080 groups Consisting of 4631 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000095388-chr10-+-84367200-84369283 l44 e 83 nr 1000000 chr ENSMUST00000121912-chr2-+-152346558-152347183 l45 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1497004 reads mapping to 522731 Unique genomic coordinates Making up 14394 groups Consisting of 4701 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148705-chr2---151366467-151368084 l45 e 84 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 940608 reads mapping to 467821 Unique genomic coordinates Making up 13154 groups Consisting of 4312 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133595-chr17-+-25965812-25968785 l44 e 85 nr 1000000 chr ENSMUST00000081381-chr8---122070800-122072285 l45 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1086945 reads mapping to 508275 Unique genomic coordinates Making up 14101 groups Consisting of 4569 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173841-chr17-+-38410399-38412086 l44 e 86 nr 1000000 chr ENSMUST00000096458-chrX-+-34851050-34851786 l43 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1036922 reads mapping to 498955 Unique genomic coordinates Making up 13872 groups Consisting of 4561 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026832-chr17-+-25965988-25968787 l44 e 87 nr 1000000 chr ENSMUST00000015157-chr8-+-125136466-125138787 l45 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1075396 reads mapping to 511022 Unique genomic coordinates Making up 14369 groups Consisting of 4775 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000089677-chr16-+-33420907-33421988 l44 e 88 nr 1000000 chr ENSMUST00000045840-chr7-+-139175268-139186088 l45 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1102855 reads mapping to 492437 Unique genomic coordinates Making up 13723 groups Consisting of 4445 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099673-chr2---102663918-102664989 l45 e 89 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 960466 reads mapping to 466040 Unique genomic coordinates Making up 13073 groups Consisting of 4240 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165838-chr17---25931516-25933990 l44 e 90 nr 1000000 chr ENSMUST00000108015-chr7-+-46788663-46795790 l43 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1195148 reads mapping to 489745 Unique genomic coordinates Making up 13601 groups Consisting of 4471 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000145030-chr17---13812667-13813291 l44 e 91 nr 1000000 chr ENSMUST00000107153-chr7-+-104808823-104811591 l45 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1108559 reads mapping to 516020 Unique genomic coordinates Making up 14461 groups Consisting of 4647 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165230-chr17-+-21563796-21565292 l44 e 92 nr 1000000 chr ENSMUST00000047622-chr6---32536804-32538192 l43 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1216980 reads mapping to 496001 Unique genomic coordinates Making up 13716 groups Consisting of 4608 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000130216-chr17-+-29172686-29173893 l44 e 93 nr 1000000 chr ENSMUST00000113876-chrX---92244276-92247993 l43 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1019825 reads mapping to 501269 Unique genomic coordinates Making up 14117 groups Consisting of 4577 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000045004-chr16-+-93751869-93753694 l44 e 94 nr 1000000 chr ENSMUST00000169020-chr8---113683199-113688294 l45 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1080251 reads mapping to 521465 Unique genomic coordinates Making up 14653 groups Consisting of 4722 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000118788-chr17-+-25000122-25001395 l44 e 95 nr 1000000 chr ENSMUST00000032874-chr7-+-89424137-89425295 l43 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1142418 reads mapping to 483474 Unique genomic coordinates Making up 13511 groups Consisting of 4338 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000089058-chr17---12427417-12431596 l44 e 96 nr 1000000 chr ENSMUST00000145172-chr3---88356152-88356996 l43 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1495564 reads mapping to 520225 Unique genomic coordinates Making up 14407 groups Consisting of 4701 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102665-chr17---37147691-37149897 l44 e 97 nr 1000000 chr ENSMUST00000032159-chr6---102216868-102217997 l45 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1358772 reads mapping to 495402 Unique genomic coordinates Making up 13720 groups Consisting of 4508 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000023713-chr15---101380130-101381098 l46 e 98 nr 1000000 chr ENSMUST00000033040-chr7-+-105031482-105032598 l45 e 98 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1269217 reads mapping to 498192 Unique genomic coordinates Making up 13946 groups Consisting of 4602 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000087056-chr17---45585884-45586999 l44 e 99 nr 1000000 chr ENSMUST00000046461-chr8---97387728-97391899 l43 e 99 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1095706 reads mapping to 501616 Unique genomic coordinates Making up 13931 groups Consisting of 4531 clusters