BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep4.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep4/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 3,487,722 number of mapped reads = 3,487,722 (100%) number of secondary alignments = 0 number of mapped bases = 22,115,446,977 bp number of sequenced bases = 2,037,816,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,124,622 duplication rate = 34.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.6755 >>>>>>> ACTG content number of A's = 486,516,270 bp (23.87%) number of C's = 520,097,607 bp (25.52%) number of T's = 507,558,330 bp (24.91%) number of G's = 523,644,181 bp (25.7%) number of N's = 0 bp (0%) GC percentage = 51.22% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 75,997,876 number of insertions = 16,367,661 mapped reads with insertion percentage = 91.09% number of deletions = 25,271,979 mapped reads with deletion percentage = 96.02% homopolymer indels = 33.78% >>>>>>> Coverage mean coverageData = 7.1096X std coverageData = 83.7307X There is a 1.18% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.1% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 2390961065 9.60393407726594 48.6830351944105 chr10 133797422 538928254 4.027941988299296 23.833784831418793 chr11 135086622 1391021374 10.297254853260007 139.36963238658586 chr12 133275309 1053245509 7.902780469261565 64.53166092603549 chr13 114364328 240033340 2.0988479904328208 12.438811336601301 chr14 107043718 887595770 8.291899670375798 71.02014763512118 chr15 101991189 545875362 5.352181569331445 89.98793964240195 chr16 90338345 819375038 9.070069171623633 153.57089661886695 chr17 83257441 893363694 10.730136349014138 84.36258894424738 chr18 80373285 635462644 7.906391333886627 88.98666885249244 chr19 58617616 2272697253 38.77157428237955 206.69551974843614 chr2 242193529 1589162478 6.561539792419475 133.5344337183962 chr20 64444167 456338435 7.0811441320981 70.10013659827018 chr21 46709983 502227420 10.75203602621735 126.79965523385829 chr22 50818468 421461620 8.293473545877061 50.86749629310948 chr3 198295559 1459398309 7.359712523869483 57.775070175727905 chr4 190214555 525858981 2.764557007743177 31.74605775980998 chr5 181538259 1186213752 6.534235585017922 65.60607730261904 chr6 170805979 950975004 5.567574446559625 55.36644321531365 chr7 159345973 1026523030 6.442102117008003 53.368163561542126 chr8 145138636 647603267 4.461963298318444 25.39420710357897 chr9 138394717 707323565 5.110914493939823 80.7972838221659 chrIS 10567884 0 0.0 0.0 chrM 16569 7456355 450.0184078701189 635.3509351705475 chrX 156040895 536512271 3.438279888102411 46.11762774000926 chrY 57227415 246851 0.00431350953035359 0.02908470057113771 ERCC-00002 1061 15565318 14670.422243166824 1618.8218612115822 ERCC-00003 1023 132239 129.26588465298144 13.501875549895876 ERCC-00004 523 2082262 3981.380497131931 549.2032459451186 ERCC-00009 984 553349 562.3465447154472 61.74747417505331 ERCC-00012 994 0 0.0 0.0 ERCC-00013 808 2182 2.7004950495049505 0.6181729374614707 ERCC-00014 1957 719 0.3673990802248339 0.48097076857728693 ERCC-00016 844 0 0.0 0.0 ERCC-00017 1136 0 0.0 0.0 ERCC-00019 644 20704 32.149068322981364 3.612639627544904 ERCC-00022 751 83983 111.82822902796272 13.434431689345203 ERCC-00024 536 526 0.9813432835820896 0.19510323078210984 ERCC-00025 1994 1984 0.9949849548645938 0.10463071725683165 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 5694 5.587831207065751 0.7539138805658978 ERCC-00035 1130 27232 24.09911504424779 2.240795689540867 ERCC-00039 740 2179 2.9445945945945944 0.44397393628381254 ERCC-00040 744 132 0.1774193548387097 0.37974652443893125 ERCC-00041 1122 0 0.0 0.0 ERCC-00042 1023 50318 49.18670576735093 4.828104040097566 ERCC-00043 1023 25074 24.51026392961877 2.394529463742064 ERCC-00044 1156 12832 11.100346020761245 1.1189238210686618 ERCC-00046 522 7843018 15024.938697318008 1931.1332483104713 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 9767 35.64598540145985 6.411540432008445 ERCC-00053 1023 11846 11.579667644183774 1.491727616909645 ERCC-00054 274 2286 8.343065693430656 1.6266485181070436 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 0 0.0 0.0 ERCC-00059 525 15268 29.081904761904763 3.996355255579528 ERCC-00060 523 253891 485.4512428298279 69.27789131730853 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 27291 26.677419354838708 3.0269394506856075 ERCC-00067 644 3752 5.826086956521739 0.7631730880349779 ERCC-00069 1137 0 0.0 0.0 ERCC-00071 642 45493 70.8613707165109 8.079087298425872 ERCC-00073 603 589 0.9767827529021559 0.15059285021222552 ERCC-00074 522 18410015 35268.227969348656 4471.430522835201 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 162251 252.72741433021807 28.718825840849142 ERCC-00077 273 0 0.0 0.0 ERCC-00078 993 10226 10.298086606243706 1.7057662104836366 ERCC-00079 644 56949 88.43012422360249 10.28290965959902 ERCC-00081 534 0 0.0 0.0 ERCC-00083 1022 0 0.0 0.0 ERCC-00084 994 1551 1.5603621730382293 1.0491626569058032 ERCC-00085 844 0 0.0 0.0 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 143681 127.83007117437722 20.317298110697884 ERCC-00095 521 71675 137.57197696737043 17.842743953104208 ERCC-00096 1107 13626826 12309.689250225836 1317.196754389955 ERCC-00097 523 1034 1.977055449330784 0.2608173571718716 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 5344 3.9585185185185185 0.44945081562424266 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 198423 194.15166340508807 20.48829448579608 ERCC-00109 536 0 0.0 0.0 ERCC-00111 994 174314 175.3661971830986 17.164644822466556 ERCC-00112 1136 26600 23.41549295774648 2.474352672235259 ERCC-00113 840 1998848 2379.5809523809526 237.70301808613118 ERCC-00116 1991 2078 1.043696634856856 1.4058400350023854 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 0 0.0 0.0 ERCC-00130 1059 5751928 5431.47119924457 545.1140654012704 ERCC-00131 771 58019 75.25162127107653 8.19616358272391 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 458819 444.161665053243 39.52602780601716 ERCC-00137 537 1040 1.9366852886405959 0.38006166853529855 ERCC-00138 1024 0 0.0 0.0 ERCC-00142 493 0 0.0 0.0 ERCC-00143 784 1381 1.7614795918367347 0.46552278286917714 ERCC-00144 538 26002 48.33085501858736 7.003828955931603 ERCC-00145 1042 131000 125.71976967370442 13.577044234114272 ERCC-00147 1023 0 0.0 0.0 ERCC-00148 494 7060 14.291497975708502 2.2258481912445576 ERCC-00150 743 2884 3.8815612382234184 0.6141647994362658 ERCC-00154 537 3165 5.893854748603352 0.782082999780067 ERCC-00156 494 485 0.9817813765182186 0.15407238852702818 ERCC-00157 1019 3246 3.185475956820412 0.8540353577095746 ERCC-00158 1027 0 0.0 0.0 ERCC-00160 743 15393 20.71736204576043 2.6035861714562283 ERCC-00162 523 17685 33.814531548757174 4.347436948573079 ERCC-00163 543 19028 35.042357274401475 4.897000836969215 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 43620 50.022935779816514 5.650421029143028 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 8091 7.909090909090909 1.103463118547467 ERCC-00171 505 3197359 6331.40396039604 940.5636664146434 GL000008.2 209709 716066 3.41456971326934 3.3993891529418288 GL000009.2 201709 0 0.0 0.0 GL000194.1 191469 1513591 7.905149136413727 7.900988424619937 GL000195.1 182896 113296 0.6194558656285539 0.8628712816887892 GL000205.2 185591 214583 1.1562144716069207 1.7081728965704845 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 8501 0.061727588260067676 0.10027035802680449 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 518571 3.217999714546346 3.2451823112294607 GL000219.1 179198 290777 1.62265761894664 2.5050021527106434 GL000220.1 161802 180573 1.1160121630140543 1.7825389198892763 GL000221.1 155397 563 0.003622978564579754 0.05938688462196905 GL000224.1 179693 409486 2.278808857328889 3.53606501769544 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 76120 0.6765921514599351 0.6766408802421379 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 278 0.01225263343470404 0.10902997549488384 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 361 0.0020622090200222787 0.04505010172763908 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 8777 0.20793650793650795 0.3736595131504651 KI270712.1 176043 8313 0.04722141749458939 0.11484544665421531 KI270713.1 40745 27067 0.6643023683887593 0.8078903488710734 KI270714.1 41717 779 0.01867344248148237 0.1341703537993274 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 3108 0.08167341146791401 0.12113393566558164 KI270719.1 176845 0 0.0 0.0 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 611 0.0060907532198253515 0.13292894341020636 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 260 5.800360514715069E-4 0.02332480421418846 KI270728.1 1872759 13419 0.007165364043104318 0.08034294246277028 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 327072 1.8193712035244642 3.048552259353387 KI270734.1 165050 1340509 8.121835807331111 22.468799846908077 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 467221 2.967763859952233 3.067991814659132 KI270742.1 186739 1241251 6.646983222572682 6.62922665793735 KI270743.1 210658 4007651 19.024442461240493 18.989148979876145 KI270744.1 168472 6906 0.040991974927584406 0.06491656542691394 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 8948 0.09588409897022107 0.12341117355960125 KI270749.1 158759 0 0.0 0.0 KI270750.1 148850 0 0.0 0.0 KI270751.1 150742 37946 0.25172811824176405 0.2601073435961581 KI270752.1 27745 206405 7.439358442962696 7.398100323267209 KI270753.1 62944 0 0.0 0.0 KI270754.1 40191 0 0.0 0.0 KI270755.1 36723 388 0.010565585600304985 0.10066820928140123 KI270756.1 79590 67131 0.8434602336977007 0.8400818467501756 KI270757.1 71251 0 0.0 0.0 SIRVome_isoforms 231019 346353860 1499.244044862111 1520.953957853764