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 458358 reads mapping to 175816 Unique genomic coordinates Making up 4218 groups Consisting of 1162 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 326529 reads mapping to 176542 Unique genomic coordinates Making up 4196 groups Consisting of 1111 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 433974 reads mapping to 197139 Unique genomic coordinates Making up 4712 groups Consisting of 1386 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 483709 reads mapping to 186158 Unique genomic coordinates Making up 4448 groups Consisting of 1282 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 398967 reads mapping to 193986 Unique genomic coordinates Making up 4660 groups Consisting of 1328 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028944-chr2---150450035-150453605 l45 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 619625 reads mapping to 194053 Unique genomic coordinates Making up 4679 groups Consisting of 1268 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125366-chr2-+-152529858-152534406 l45 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 645230 reads mapping to 182507 Unique genomic coordinates Making up 4266 groups Consisting of 1174 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000031967-chr6---40468532-40469507 l43 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 577686 reads mapping to 191760 Unique genomic coordinates Making up 4594 groups Consisting of 1268 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 498520 reads mapping to 183937 Unique genomic coordinates Making up 4360 groups Consisting of 1170 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098970-chr9---20245273-20247209 l43 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 527155 reads mapping to 187344 Unique genomic coordinates Making up 4440 groups Consisting of 1275 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161388-chr5-+-150552506-150553710 l45 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 564715 reads mapping to 179511 Unique genomic coordinates Making up 4220 groups Consisting of 1150 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 413993 reads mapping to 188116 Unique genomic coordinates Making up 4531 groups Consisting of 1354 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167014-chr9---86717723-86720412 l43 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 572965 reads mapping to 194418 Unique genomic coordinates Making up 4638 groups Consisting of 1248 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 391453 reads mapping to 191480 Unique genomic coordinates Making up 4583 groups Consisting of 1245 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 421903 reads mapping to 192670 Unique genomic coordinates Making up 4592 groups Consisting of 1300 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 463826 reads mapping to 197310 Unique genomic coordinates Making up 4703 groups Consisting of 1345 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 431276 reads mapping to 190090 Unique genomic coordinates Making up 4544 groups Consisting of 1277 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000137488-chr7---148614674-148615317 l45 e 17 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 584609 reads mapping to 194900 Unique genomic coordinates Making up 4658 groups Consisting of 1339 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170869-chr5-+-13472899-13474018 l43 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 610507 reads mapping to 192388 Unique genomic coordinates Making up 4633 groups Consisting of 1314 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 443849 reads mapping to 195517 Unique genomic coordinates Making up 4627 groups Consisting of 1253 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 391715 reads mapping to 180821 Unique genomic coordinates Making up 4379 groups Consisting of 1232 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 408611 reads mapping to 175102 Unique genomic coordinates Making up 4195 groups Consisting of 1197 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000148081-chr4---120440198-120440822 l45 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 717983 reads mapping to 193037 Unique genomic coordinates Making up 4634 groups Consisting of 1305 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 354438 reads mapping to 191359 Unique genomic coordinates Making up 4532 groups Consisting of 1247 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 422493 reads mapping to 193962 Unique genomic coordinates Making up 4643 groups Consisting of 1276 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 424229 reads mapping to 184600 Unique genomic coordinates Making up 4390 groups Consisting of 1206 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 446811 reads mapping to 198177 Unique genomic coordinates Making up 4694 groups Consisting of 1293 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 351929 reads mapping to 181517 Unique genomic coordinates Making up 4379 groups Consisting of 1247 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000070980-chr7---138288861-138289828 l45 e 28 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 584224 reads mapping to 186395 Unique genomic coordinates Making up 4423 groups Consisting of 1190 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000099742-chr16-+-44401034-44402129 l44 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 691560 reads mapping to 185914 Unique genomic coordinates Making up 4329 groups Consisting of 1212 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 445654 reads mapping to 196230 Unique genomic coordinates Making up 4685 groups Consisting of 1306 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 412366 reads mapping to 199879 Unique genomic coordinates Making up 4669 groups Consisting of 1272 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 369809 reads mapping to 184972 Unique genomic coordinates Making up 4385 groups Consisting of 1195 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000059555-chr9-+-54996661-54998133 l43 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 519776 reads mapping to 190420 Unique genomic coordinates Making up 4552 groups Consisting of 1256 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 403167 reads mapping to 187886 Unique genomic coordinates Making up 4449 groups Consisting of 1245 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 421145 reads mapping to 188897 Unique genomic coordinates Making up 4612 groups Consisting of 1231 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 429561 reads mapping to 190429 Unique genomic coordinates Making up 4548 groups Consisting of 1283 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 345500 reads mapping to 183213 Unique genomic coordinates Making up 4451 groups Consisting of 1190 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000033497-chrX---7471645-7474038 l41 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 509907 reads mapping to 185402 Unique genomic coordinates Making up 4399 groups Consisting of 1243 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 399515 reads mapping to 190497 Unique genomic coordinates Making up 4393 groups Consisting of 1238 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 401447 reads mapping to 186310 Unique genomic coordinates Making up 4505 groups Consisting of 1254 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 439338 reads mapping to 197285 Unique genomic coordinates Making up 4730 groups Consisting of 1304 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 359880 reads mapping to 178544 Unique genomic coordinates Making up 4302 groups Consisting of 1147 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 340949 reads mapping to 190264 Unique genomic coordinates Making up 4582 groups Consisting of 1264 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 386753 reads mapping to 187473 Unique genomic coordinates Making up 4561 groups Consisting of 1212 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 392266 reads mapping to 194682 Unique genomic coordinates Making up 4653 groups Consisting of 1320 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 446925 reads mapping to 194356 Unique genomic coordinates Making up 4610 groups Consisting of 1316 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 386780 reads mapping to 184917 Unique genomic coordinates Making up 4494 groups Consisting of 1274 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 340355 reads mapping to 185138 Unique genomic coordinates Making up 4492 groups Consisting of 1287 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039135-chr14---68395130-68396249 l44 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 731963 reads mapping to 189860 Unique genomic coordinates Making up 4571 groups Consisting of 1263 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 495942 reads mapping to 193163 Unique genomic coordinates Making up 4699 groups Consisting of 1301 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 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 686349 reads mapping to 179209 Unique genomic coordinates Making up 4312 groups Consisting of 1210 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000160888-chr5-+-29522532-29523152 l43 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 629414 reads mapping to 197802 Unique genomic coordinates Making up 4713 groups Consisting of 1390 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 378484 reads mapping to 192613 Unique genomic coordinates Making up 4612 groups Consisting of 1289 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 365388 reads mapping to 195213 Unique genomic coordinates Making up 4593 groups Consisting of 1243 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000101460-chr12-+-41394493-41396155 l44 e 55 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 783352 reads mapping to 182873 Unique genomic coordinates Making up 4373 groups Consisting of 1205 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000034987-chr9-+-86417331-86418456 l43 e 56 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 584116 reads mapping to 193532 Unique genomic coordinates Making up 4510 groups Consisting of 1326 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 370960 reads mapping to 195217 Unique genomic coordinates Making up 4720 groups Consisting of 1350 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 413780 reads mapping to 182403 Unique genomic coordinates Making up 4292 groups Consisting of 1233 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000168164-chr8---13104275-13105459 l43 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 552342 reads mapping to 184926 Unique genomic coordinates Making up 4468 groups Consisting of 1236 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 426445 reads mapping to 185025 Unique genomic coordinates Making up 4452 groups Consisting of 1218 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 381574 reads mapping to 185562 Unique genomic coordinates Making up 4423 groups Consisting of 1288 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000063243-chr7---52649529-52651062 l43 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 577656 reads mapping to 190513 Unique genomic coordinates Making up 4463 groups Consisting of 1240 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 459680 reads mapping to 183394 Unique genomic coordinates Making up 4376 groups Consisting of 1207 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 492594 reads mapping to 191999 Unique genomic coordinates Making up 4497 groups Consisting of 1270 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 445838 reads mapping to 183139 Unique genomic coordinates Making up 4237 groups Consisting of 1171 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 280593 reads mapping to 166293 Unique genomic coordinates Making up 3991 groups Consisting of 1028 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 364043 reads mapping to 188879 Unique genomic coordinates Making up 4601 groups Consisting of 1318 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 421516 reads mapping to 193506 Unique genomic coordinates Making up 4604 groups Consisting of 1274 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 463553 reads mapping to 178975 Unique genomic coordinates Making up 4304 groups Consisting of 1178 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 360882 reads mapping to 174671 Unique genomic coordinates Making up 4186 groups Consisting of 1175 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 407349 reads mapping to 185370 Unique genomic coordinates Making up 4504 groups Consisting of 1215 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000049810-chr9-+-123718549-123720872 l45 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 513237 reads mapping to 193944 Unique genomic coordinates Making up 4505 groups Consisting of 1346 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 380402 reads mapping to 187089 Unique genomic coordinates Making up 4450 groups Consisting of 1213 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000168203-chr7---144391566-144393374 l45 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 554819 reads mapping to 191162 Unique genomic coordinates Making up 4506 groups Consisting of 1275 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000075806-chr16---29260503-29261575 l44 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 934741 reads mapping to 188345 Unique genomic coordinates Making up 4439 groups Consisting of 1229 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028178-chr2---58147837-58149076 l43 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 930412 reads mapping to 182966 Unique genomic coordinates Making up 4298 groups Consisting of 1201 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 377949 reads mapping to 183564 Unique genomic coordinates Making up 4372 groups Consisting of 1219 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000097504-chr18---82779497-82780578 l44 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 750096 reads mapping to 204224 Unique genomic coordinates Making up 4834 groups Consisting of 1418 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 385498 reads mapping to 184376 Unique genomic coordinates Making up 4407 groups Consisting of 1223 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165771-chr7---93376190-93380280 l43 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 609221 reads mapping to 195104 Unique genomic coordinates Making up 4641 groups Consisting of 1304 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125903-chr8-+-42145158-42146281 l43 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 533851 reads mapping to 181209 Unique genomic coordinates Making up 4393 groups Consisting of 1215 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 445995 reads mapping to 194863 Unique genomic coordinates Making up 4663 groups Consisting of 1327 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 407849 reads mapping to 194412 Unique genomic coordinates Making up 4681 groups Consisting of 1273 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 352386 reads mapping to 177515 Unique genomic coordinates Making up 4291 groups Consisting of 1139 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000022566-chr14-+-61309191-61311885 l44 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 837674 reads mapping to 194392 Unique genomic coordinates Making up 4529 groups Consisting of 1284 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000014065-chr7-+-31090278-31093386 l43 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 719071 reads mapping to 194500 Unique genomic coordinates Making up 4594 groups Consisting of 1331 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 472123 reads mapping to 197907 Unique genomic coordinates Making up 4695 groups Consisting of 1299 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 412694 reads mapping to 189297 Unique genomic coordinates Making up 4458 groups Consisting of 1249 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 349476 reads mapping to 178790 Unique genomic coordinates Making up 4278 groups Consisting of 1250 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 494709 reads mapping to 184013 Unique genomic coordinates Making up 4215 groups Consisting of 1205 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000031391-chr5-+-123820527-123824091 l45 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 650053 reads mapping to 190400 Unique genomic coordinates Making up 4616 groups Consisting of 1277 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 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1864284 reads mapping to 183686 Unique genomic coordinates Making up 4352 groups Consisting of 1206 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 440494 reads mapping to 195576 Unique genomic coordinates Making up 4663 groups Consisting of 1332 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 393033 reads mapping to 198162 Unique genomic coordinates Making up 4658 groups Consisting of 1296 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 361946 reads mapping to 182515 Unique genomic coordinates Making up 4413 groups Consisting of 1249 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 459230 reads mapping to 193861 Unique genomic coordinates Making up 4645 groups Consisting of 1354 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 458899 reads mapping to 184342 Unique genomic coordinates Making up 4327 groups Consisting of 1237 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 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 803166 reads mapping to 193336 Unique genomic coordinates Making up 4432 groups Consisting of 1316 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 411709 reads mapping to 184830 Unique genomic coordinates Making up 4387 groups Consisting of 1173 clusters