BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/pacBioSII-Cshl-CapTrap_HpreCap_0+_Heart02Rep1.bam outfile = output/mappings/longReadMapping/bamqc/pacBioSII-Cshl-CapTrap_HpreCap_0+_Heart02Rep1/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 3,126,881 number of mapped reads = 3,126,881 (100%) number of secondary alignments = 0 number of mapped bases = 37,292,979,754 bp number of sequenced bases = 2,834,936,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,947,598 duplication rate = 40.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 6.9133 >>>>>>> ACTG content number of A's = 744,352,959 bp (26.26%) number of C's = 697,112,374 bp (24.59%) number of T's = 646,619,285 bp (22.81%) number of G's = 746,851,775 bp (26.34%) number of N's = 0 bp (0%) GC percentage = 50.93% >>>>>>> Mismatches and indels general error rate = 0.0002 number of mismatches = 5,023,286 number of insertions = 1,636,836 mapped reads with insertion percentage = 20.09% number of deletions = 738,732 mapped reads with deletion percentage = 12.9% homopolymer indels = 42.82% >>>>>>> Coverage mean coverageData = 11.9889X std coverageData = 213.8661X There is a 1.21% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 3680300174 14.782909171148033 98.29433833163216 chr10 133797422 1343946622 10.044637646306818 31.621064329489112 chr11 135086622 2041658722 15.113700318896123 134.70865114518955 chr12 133275309 5204852628 39.053390061920624 912.4779707783698 chr13 114364328 497734541 4.3521834972877205 71.83149887470802 chr14 107043718 871013161 8.13698531099228 33.49465307885899 chr15 101991189 1869658719 18.331570965409572 155.1398678262095 chr16 90338345 893504612 9.890646236656206 66.4365692178585 chr17 83257441 1042600429 12.522609588733337 380.81913730456694 chr18 80373285 509618337 6.340643374225652 85.42359333726729 chr19 58617616 1943554376 33.15648961226946 199.31534982168472 chr2 242193529 2514641780 10.382778558877186 36.25454128810598 chr20 64444167 651607639 10.111196549409971 38.64530117407604 chr21 46709983 428162010 9.166391903846336 52.518903545092876 chr22 50818468 1123964192 22.117238795943237 239.15177467739136 chr3 198295559 1872154204 9.441231127117678 92.79665995047026 chr4 190214555 1831363741 9.627884369836998 34.957014205254175 chr5 181538259 1872783463 10.316191602344276 40.959034847106395 chr6 170805979 1724750230 10.097715783122556 48.68781157913679 chr7 159345973 1759871325 11.044341390415935 51.9713215100458 chr8 145138636 1549142348 10.673535253562669 35.15219270427308 chr9 138394717 857436986 6.195590442950217 62.17026663417754 chrIS 10567884 0 0.0 0.0 chrM 16569 6669195 402.5104110085099 337.3198221784006 chrX 156040895 1018367111 6.526283452808958 60.23873735168979 chrY 57227415 79521323 1.3895669234754007 9.210476495620863 ERCC-00002 1061 6369069 6002.892554194156 511.53686988062015 ERCC-00003 1023 21859 21.36754643206256 1.9511327150692126 ERCC-00004 523 146515 280.1434034416826 31.407868913952882 ERCC-00009 984 148646 151.0630081300813 12.424338566280648 ERCC-00012 994 0 0.0 0.0 ERCC-00013 808 0 0.0 0.0 ERCC-00014 1957 0 0.0 0.0 ERCC-00016 844 834 0.9881516587677726 0.1082033180742259 ERCC-00017 1136 0 0.0 0.0 ERCC-00019 644 1906 2.959627329192547 0.3411487502719627 ERCC-00022 751 20820 27.723035952063913 2.610073634024117 ERCC-00024 536 0 0.0 0.0 ERCC-00025 1994 4515 2.264292878635908 0.4623776425914766 ERCC-00028 1130 0 0.0 0.0 ERCC-00031 1138 0 0.0 0.0 ERCC-00033 2022 0 0.0 0.0 ERCC-00034 1019 6065 5.951913640824338 0.5229227969974322 ERCC-00035 1130 7847 6.944247787610619 0.6039348096340578 ERCC-00039 740 740 1.0 0.0 ERCC-00040 744 0 0.0 0.0 ERCC-00041 1122 0 0.0 0.0 ERCC-00042 1023 10909 10.663734115347019 1.209002941996046 ERCC-00043 1023 22170 21.671554252199414 1.3252893434625346 ERCC-00044 1156 3450 2.9844290657439445 0.20317489351756213 ERCC-00046 522 413891 792.8946360153257 94.37358748411039 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 0 0.0 0.0 ERCC-00053 1023 0 0.0 0.0 ERCC-00054 274 0 0.0 0.0 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 0 0.0 0.0 ERCC-00059 525 5175 9.857142857142858 1.0899666099859948 ERCC-00060 523 5140 9.82791586998088 1.2571116461233172 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 6091 5.95405669599218 0.496073318320172 ERCC-00067 644 0 0.0 0.0 ERCC-00069 1137 1391 1.2233948988566403 0.43104839946676676 ERCC-00071 642 9300 14.485981308411215 1.5984405158056672 ERCC-00073 603 0 0.0 0.0 ERCC-00074 522 806500 1545.0191570881227 183.2444161959604 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 25803 40.191588785046726 4.187300932172563 ERCC-00077 273 0 0.0 0.0 ERCC-00078 993 7090 7.139979859013092 0.7330101821167182 ERCC-00079 644 7633 11.852484472049689 1.2791968441885304 ERCC-00081 534 0 0.0 0.0 ERCC-00083 1022 0 0.0 0.0 ERCC-00084 994 0 0.0 0.0 ERCC-00085 844 0 0.0 0.0 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 58049 51.645017793594306 4.067275981900426 ERCC-00095 521 2835 5.4414587332053745 0.7719463291274135 ERCC-00096 1107 5446905 4920.420054200542 408.64898545608366 ERCC-00097 523 515 0.9847036328871893 0.13700179057493542 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 1339 0.9918518518518519 0.08989858636210027 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 124349 121.67221135029354 10.009362395514437 ERCC-00109 536 0 0.0 0.0 ERCC-00111 994 94279 94.84808853118712 8.333037826040632 ERCC-00112 1136 29893 26.31426056338028 2.1136787893266864 ERCC-00113 840 627348 746.8428571428572 64.34195000629268 ERCC-00116 1991 7939 3.9874434957307887 0.2203669003391311 ERCC-00117 1136 0 0.0 0.0 ERCC-00120 536 0 0.0 0.0 ERCC-00123 1022 0 0.0 0.0 ERCC-00126 1118 1109 0.9919499105545617 0.10726369159399407 ERCC-00130 1059 2464903 2327.576015108593 168.50100766397017 ERCC-00131 771 28624 37.125810635538265 3.3855293023704616 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 221935 214.84511132623427 15.5561155097781 ERCC-00137 537 0 0.0 0.0 ERCC-00138 1024 0 0.0 0.0 ERCC-00142 493 0 0.0 0.0 ERCC-00143 784 2323 2.9630102040816326 0.3271851499454952 ERCC-00144 538 2643 4.912639405204461 0.643662343141829 ERCC-00145 1042 50620 48.57965451055662 4.172465721602034 ERCC-00147 1023 0 0.0 0.0 ERCC-00148 494 970 1.9635627530364372 0.2598042300750508 ERCC-00150 743 0 0.0 0.0 ERCC-00154 537 1060 1.9739292364990688 0.2268520273048959 ERCC-00156 494 0 0.0 0.0 ERCC-00157 1019 1011 0.9921491658488715 0.08825643633333574 ERCC-00158 1027 0 0.0 0.0 ERCC-00160 743 5148 6.928667563930014 0.6367178847195881 ERCC-00162 523 515 0.9847036328871893 0.12272892188054466 ERCC-00163 543 1607 2.9594843462246776 0.33248776077777753 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 17117 19.629587155963304 1.9405957067992565 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 2030 1.9843597262952102 0.17617017127771292 ERCC-00171 505 449009 889.1267326732673 109.44109559287175 GL000008.2 209709 247 0.0011778226017958218 0.03429920313527007 GL000009.2 201709 0 0.0 0.0 GL000194.1 191469 4227002 22.07669126594906 22.113264753688576 GL000195.1 182896 628941 3.438790350800455 3.753817604512794 GL000205.2 185591 452507 2.438194740046662 2.928775722953696 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 8341 0.0605657938686301 0.09475099063474524 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 2272413 14.10149118506705 14.106091649091784 GL000219.1 179198 149716 0.8354780745320818 0.909952239702994 GL000220.1 161802 44807 0.27692488349958594 1.1013349892655748 GL000221.1 155397 0 0.0 0.0 GL000224.1 179693 0 0.0 0.0 GL000225.1 211173 0 0.0 0.0 GL000226.1 15008 0 0.0 0.0 KI270302.1 2274 0 0.0 0.0 KI270303.1 1942 0 0.0 0.0 KI270304.1 2165 0 0.0 0.0 KI270305.1 1472 0 0.0 0.0 KI270310.1 1201 0 0.0 0.0 KI270311.1 12399 0 0.0 0.0 KI270312.1 998 0 0.0 0.0 KI270315.1 2276 0 0.0 0.0 KI270316.1 1444 0 0.0 0.0 KI270317.1 37690 0 0.0 0.0 KI270320.1 4416 0 0.0 0.0 KI270322.1 21476 0 0.0 0.0 KI270329.1 1040 0 0.0 0.0 KI270330.1 1652 0 0.0 0.0 KI270333.1 2699 0 0.0 0.0 KI270334.1 1368 0 0.0 0.0 KI270335.1 1048 0 0.0 0.0 KI270336.1 1026 0 0.0 0.0 KI270337.1 1121 0 0.0 0.0 KI270338.1 1428 0 0.0 0.0 KI270340.1 1428 0 0.0 0.0 KI270362.1 3530 0 0.0 0.0 KI270363.1 1803 0 0.0 0.0 KI270364.1 2855 0 0.0 0.0 KI270366.1 8320 0 0.0 0.0 KI270371.1 2805 0 0.0 0.0 KI270372.1 1650 0 0.0 0.0 KI270373.1 1451 0 0.0 0.0 KI270374.1 2656 0 0.0 0.0 KI270375.1 2378 0 0.0 0.0 KI270376.1 1136 0 0.0 0.0 KI270378.1 1048 0 0.0 0.0 KI270379.1 1045 0 0.0 0.0 KI270381.1 1930 0 0.0 0.0 KI270382.1 4215 0 0.0 0.0 KI270383.1 1750 0 0.0 0.0 KI270384.1 1658 0 0.0 0.0 KI270385.1 990 0 0.0 0.0 KI270386.1 1788 0 0.0 0.0 KI270387.1 1537 0 0.0 0.0 KI270388.1 1216 0 0.0 0.0 KI270389.1 1298 0 0.0 0.0 KI270390.1 2387 0 0.0 0.0 KI270391.1 1484 0 0.0 0.0 KI270392.1 971 0 0.0 0.0 KI270393.1 1308 0 0.0 0.0 KI270394.1 970 0 0.0 0.0 KI270395.1 1143 0 0.0 0.0 KI270396.1 1880 0 0.0 0.0 KI270411.1 2646 0 0.0 0.0 KI270412.1 1179 0 0.0 0.0 KI270414.1 2489 0 0.0 0.0 KI270417.1 2043 0 0.0 0.0 KI270418.1 2145 0 0.0 0.0 KI270419.1 1029 0 0.0 0.0 KI270420.1 2321 0 0.0 0.0 KI270422.1 1445 0 0.0 0.0 KI270423.1 981 0 0.0 0.0 KI270424.1 2140 0 0.0 0.0 KI270425.1 1884 0 0.0 0.0 KI270429.1 1361 0 0.0 0.0 KI270435.1 92983 0 0.0 0.0 KI270438.1 112505 0 0.0 0.0 KI270442.1 392061 0 0.0 0.0 KI270448.1 7992 0 0.0 0.0 KI270465.1 1774 0 0.0 0.0 KI270466.1 1233 0 0.0 0.0 KI270467.1 3920 0 0.0 0.0 KI270468.1 4055 0 0.0 0.0 KI270507.1 5353 0 0.0 0.0 KI270508.1 1951 0 0.0 0.0 KI270509.1 2318 0 0.0 0.0 KI270510.1 2415 0 0.0 0.0 KI270511.1 8127 0 0.0 0.0 KI270512.1 22689 0 0.0 0.0 KI270515.1 6361 0 0.0 0.0 KI270516.1 1300 0 0.0 0.0 KI270517.1 3253 0 0.0 0.0 KI270518.1 2186 0 0.0 0.0 KI270519.1 138126 0 0.0 0.0 KI270521.1 7642 0 0.0 0.0 KI270522.1 5674 0 0.0 0.0 KI270528.1 2983 0 0.0 0.0 KI270529.1 1899 0 0.0 0.0 KI270530.1 2168 0 0.0 0.0 KI270538.1 91309 0 0.0 0.0 KI270539.1 993 0 0.0 0.0 KI270544.1 1202 0 0.0 0.0 KI270548.1 1599 0 0.0 0.0 KI270579.1 31033 0 0.0 0.0 KI270580.1 1553 0 0.0 0.0 KI270581.1 7046 0 0.0 0.0 KI270582.1 6504 0 0.0 0.0 KI270583.1 1400 0 0.0 0.0 KI270584.1 4513 0 0.0 0.0 KI270587.1 2969 0 0.0 0.0 KI270588.1 6158 0 0.0 0.0 KI270589.1 44474 0 0.0 0.0 KI270590.1 4685 0 0.0 0.0 KI270591.1 5796 0 0.0 0.0 KI270593.1 3041 0 0.0 0.0 KI270706.1 175055 320306 1.8297449373054182 1.8141286389345492 KI270707.1 32032 0 0.0 0.0 KI270708.1 127682 0 0.0 0.0 KI270709.1 66860 0 0.0 0.0 KI270710.1 40176 0 0.0 0.0 KI270711.1 42210 0 0.0 0.0 KI270712.1 176043 0 0.0 0.0 KI270713.1 40745 12840 0.3151306908823168 0.3790736238386489 KI270714.1 41717 0 0.0 0.0 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 0 0.0 0.0 KI270718.1 38054 0 0.0 0.0 KI270719.1 176845 0 0.0 0.0 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 62146 0.6195023725028909 2.4417784089619037 KI270722.1 194050 0 0.0 0.0 KI270723.1 38115 0 0.0 0.0 KI270724.1 39555 0 0.0 0.0 KI270725.1 172810 0 0.0 0.0 KI270726.1 43739 0 0.0 0.0 KI270727.1 448248 27105 0.06046875836590459 0.08982740370144084 KI270728.1 1872759 214655 0.11461966008439954 0.3701437785750026 KI270729.1 280839 0 0.0 0.0 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 0 0.0 0.0 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 79221 0.4406748548161004 1.4826542913784608 KI270734.1 165050 2407228 14.584840957285671 35.32838891507684 KI270735.1 42811 0 0.0 0.0 KI270736.1 181920 0 0.0 0.0 KI270737.1 103838 0 0.0 0.0 KI270738.1 99375 0 0.0 0.0 KI270739.1 73985 0 0.0 0.0 KI270740.1 37240 0 0.0 0.0 KI270741.1 157432 35036 0.22254687738198078 0.24241993008490645 KI270742.1 186739 2285872 12.24099946984829 12.174720625139994 KI270743.1 210658 0 0.0 0.0 KI270744.1 168472 96003 0.5698454342561375 0.7647443335046569 KI270745.1 41891 0 0.0 0.0 KI270746.1 66486 0 0.0 0.0 KI270747.1 198735 0 0.0 0.0 KI270748.1 93321 0 0.0 0.0 KI270749.1 158759 0 0.0 0.0 KI270750.1 148850 0 0.0 0.0 KI270751.1 150742 53742 0.356516432049462 0.3784290762718512 KI270752.1 27745 0 0.0 0.0 KI270753.1 62944 0 0.0 0.0 KI270754.1 40191 0 0.0 0.0 KI270755.1 36723 0 0.0 0.0 KI270756.1 79590 0 0.0 0.0 KI270757.1 71251 0 0.0 0.0 SIRVome_isoforms 231019 73026324 316.1052727264857 340.0782911297041