BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain02Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-CapTrap_HpreCap_0+_Brain02Rep1/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 13,840,799 number of mapped reads = 13,840,799 (100%) number of secondary alignments = 0 number of mapped bases = 120,966,771,698 bp number of sequenced bases = 8,932,451,686 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,493,488 duplication rate = 37.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.8315 >>>>>>> ACTG content number of A's = 2,199,388,184 bp (24.62%) number of C's = 2,232,293,711 bp (24.99%) number of T's = 2,252,122,778 bp (25.21%) number of G's = 2,248,647,013 bp (25.17%) number of N's = 0 bp (0%) GC percentage = 50.16% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 332,372,259 number of insertions = 67,544,964 mapped reads with insertion percentage = 91.67% number of deletions = 109,767,844 mapped reads with deletion percentage = 96.32% homopolymer indels = 34.19% >>>>>>> Coverage mean coverageData = 38.8882X std coverageData = 291.7917X There is a 4.87% of reference with a coverageData >= 1X There is a 3% of reference with a coverageData >= 2X There is a 2.15% of reference with a coverageData >= 3X There is a 1.71% of reference with a coverageData >= 4X There is a 1.45% of reference with a coverageData >= 5X There is a 1.28% of reference with a coverageData >= 6X There is a 1.15% of reference with a coverageData >= 7X There is a 1.06% of reference with a coverageData >= 8X There is a 0.98% of reference with a coverageData >= 9X There is a 0.91% of reference with a coverageData >= 10X There is a 0.86% of reference with a coverageData >= 11X There is a 0.81% of reference with a coverageData >= 12X There is a 0.77% of reference with a coverageData >= 13X There is a 0.73% of reference with a coverageData >= 14X There is a 0.7% of reference with a coverageData >= 15X There is a 0.67% of reference with a coverageData >= 16X There is a 0.64% of reference with a coverageData >= 17X There is a 0.62% of reference with a coverageData >= 18X There is a 0.6% of reference with a coverageData >= 19X There is a 0.58% of reference with a coverageData >= 20X There is a 0.56% of reference with a coverageData >= 21X There is a 0.55% of reference with a coverageData >= 22X There is a 0.53% of reference with a coverageData >= 23X There is a 0.51% of reference with a coverageData >= 24X There is a 0.5% of reference with a coverageData >= 25X There is a 0.49% of reference with a coverageData >= 26X There is a 0.48% of reference with a coverageData >= 27X There is a 0.46% of reference with a coverageData >= 28X There is a 0.45% of reference with a coverageData >= 29X There is a 0.44% of reference with a coverageData >= 30X There is a 0.44% of reference with a coverageData >= 31X There is a 0.43% of reference with a coverageData >= 32X There is a 0.42% of reference with a coverageData >= 33X There is a 0.41% of reference with a coverageData >= 34X There is a 0.4% of reference with a coverageData >= 35X There is a 0.39% of reference with a coverageData >= 36X There is a 0.39% of reference with a coverageData >= 37X There is a 0.38% of reference with a coverageData >= 38X There is a 0.37% of reference with a coverageData >= 39X There is a 0.37% of reference with a coverageData >= 40X There is a 0.36% of reference with a coverageData >= 41X There is a 0.36% of reference with a coverageData >= 42X There is a 0.35% of reference with a coverageData >= 43X There is a 0.34% of reference with a coverageData >= 44X There is a 0.34% of reference with a coverageData >= 45X There is a 0.33% of reference with a coverageData >= 46X There is a 0.33% of reference with a coverageData >= 47X There is a 0.32% of reference with a coverageData >= 48X There is a 0.32% of reference with a coverageData >= 49X There is a 0.32% of reference with a coverageData >= 50X There is a 0.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 10782538008 43.31094543124499 168.85134415056896 chr10 133797422 4245076575 31.72764102285917 118.97544064449089 chr11 135086622 6411656345 47.463296143418255 325.77411956539993 chr12 133275309 5928284869 44.48149408529978 250.78501009891184 chr13 114364328 2390506138 20.902550470108128 161.54274500841186 chr14 107043718 5221688375 48.780895063828034 235.35684420472936 chr15 101991189 4089022224 40.09191641054405 332.7065569686816 chr16 90338345 3759692636 41.617904733587935 513.1946226041251 chr17 83257441 6044185955 72.59634553264735 410.23011318470725 chr18 80373285 1510094087 18.788507736121524 115.80314957620992 chr19 58617616 7123534308 121.52548660457293 710.5979000475336 chr2 242193529 9953254284 41.096284963088344 365.63442708949907 chr20 64444167 3054213883 47.39317808235461 207.03036409969587 chr21 46709983 1670089562 35.7544459393188 142.42477130726348 chr22 50818468 3674771137 72.31172606383963 254.51862868889117 chr3 198295559 7665276171 38.65581362313818 252.05614047941694 chr4 190214555 3940066847 20.713803141930963 124.05397623568092 chr5 181538259 6936002969 38.206838642205994 244.857938670457 chr6 170805979 7703494114 45.10084576137701 404.87726639382527 chr7 159345973 5324761112 33.4163519275131 155.6248258984764 chr8 145138636 4730797696 32.59502656480801 200.62566609337208 chr9 138394717 4548778100 32.86814842794902 492.952038541677 chrIS 10567884 0 0.0 0.0 chrM 16569 10318083 622.7342024262176 566.9126587345067 chrX 156040895 3339831738 21.403566917505824 152.25237955312906 chrY 57227415 286404196 5.004667710397193 29.36961665297715 ERCC-00002 1061 52697648 49667.90574929312 5747.543522053976 ERCC-00003 1023 10414 10.179863147605083 3.094568903602806 ERCC-00004 523 161621 309.0267686424474 43.71277030171323 ERCC-00009 984 1284691 1305.5802845528456 136.64361682582486 ERCC-00012 994 0 0.0 0.0 ERCC-00013 808 1930 2.3886138613861387 0.7748117840203517 ERCC-00014 1957 387 0.19775166070516095 0.3983038305031874 ERCC-00016 844 0 0.0 0.0 ERCC-00017 1136 0 0.0 0.0 ERCC-00019 644 69327 107.65062111801242 12.427813535174774 ERCC-00022 751 253156 337.0918774966711 40.8284417327345 ERCC-00024 536 0 0.0 0.0 ERCC-00025 1994 9150 4.58876629889669 1.1246173581873085 ERCC-00028 1130 4151 3.6734513274336282 0.6072763426541541 ERCC-00031 1138 1807 1.5878734622144113 0.5183409666238156 ERCC-00033 2022 0 0.0 0.0 ERCC-00034 1019 22038 21.627085377821395 2.3796011786885076 ERCC-00035 1130 79862 70.67433628318584 6.917197523818556 ERCC-00039 740 2926 3.954054054054054 0.3966348586584348 ERCC-00040 744 0 0.0 0.0 ERCC-00041 1122 0 0.0 0.0 ERCC-00042 1023 12625 12.341153470185729 1.4108139035817842 ERCC-00043 1023 90395 88.36265884652981 7.269964736681631 ERCC-00044 1156 33946 29.365051903114185 2.247427486027788 ERCC-00046 522 833949 1597.603448275862 210.26550864571297 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 0 0.0 0.0 ERCC-00053 1023 3256 3.182795698924731 0.5853866722065135 ERCC-00054 274 5189 18.937956204379564 3.7245254215612458 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 1104 0.971830985915493 0.17520922964260194 ERCC-00059 525 62164 118.40761904761905 16.093239098180398 ERCC-00060 523 7113 13.60038240917782 2.0380687187581157 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 14765 14.433040078201369 1.6232489074695589 ERCC-00067 644 8186 12.711180124223603 2.1130180089825217 ERCC-00069 1137 2250 1.9788918205804749 0.2471259506088762 ERCC-00071 642 144479 225.04517133956386 24.36598167874685 ERCC-00073 603 2213 3.669983416252073 0.6961698572176004 ERCC-00074 522 921937 1766.1628352490422 227.3710196108084 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 492591 767.2757009345794 90.15093575539653 ERCC-00077 273 0 0.0 0.0 ERCC-00078 993 38542 38.813695871097686 4.866422247989883 ERCC-00079 644 194076 301.360248447205 35.92103295804316 ERCC-00081 534 0 0.0 0.0 ERCC-00083 1022 0 0.0 0.0 ERCC-00084 994 15122 15.21327967806841 2.3647047675815474 ERCC-00085 844 11151 13.212085308056873 1.7016820980045833 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 382118 339.9626334519573 43.29717196437545 ERCC-00095 521 1349 2.5892514395393476 0.5809052109354955 ERCC-00096 1107 31629436 28572.209575429086 2961.916984632068 ERCC-00097 523 0 0.0 0.0 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 3034 2.2474074074074073 0.5994208453117379 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 739013 723.1046966731898 82.63998991911515 ERCC-00109 536 718 1.3395522388059702 0.5242504116323426 ERCC-00111 994 516479 519.5965794768612 49.47208601825213 ERCC-00112 1136 128941 113.5044014084507 10.739674257068279 ERCC-00113 840 6723809 8004.534523809524 798.0806412133613 ERCC-00116 1991 17785 8.932697137117026 3.0826490795974824 ERCC-00117 1136 0 0.0 0.0 ERCC-00120 536 1036 1.9328358208955223 0.5534979594265271 ERCC-00123 1022 0 0.0 0.0 ERCC-00126 1118 5515 4.932915921288014 0.5635495624672672 ERCC-00130 1059 14728750 13908.168083097262 1422.249818703737 ERCC-00131 771 166978 216.57328145265888 26.026668889049937 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 1212545 1173.809293320426 103.69109129654899 ERCC-00137 537 526 0.9795158286778398 0.19009925385423157 ERCC-00138 1024 0 0.0 0.0 ERCC-00142 493 0 0.0 0.0 ERCC-00143 784 6934 8.84438775510204 1.1143025340735495 ERCC-00144 538 75693 140.69330855018586 19.080184224070315 ERCC-00145 1042 474784 455.6468330134357 49.12587801216475 ERCC-00147 1023 0 0.0 0.0 ERCC-00148 494 17094 34.60323886639676 4.242747895155629 ERCC-00150 743 2252 3.030955585464334 0.5870679296346667 ERCC-00154 537 5255 9.78584729981378 1.6102473726821245 ERCC-00156 494 1943 3.9331983805668016 0.5983176981540858 ERCC-00157 1019 1489 1.4612365063788026 0.5204157866336417 ERCC-00158 1027 0 0.0 0.0 ERCC-00160 743 31402 42.26379542395693 5.170547865440475 ERCC-00162 523 0 0.0 0.0 ERCC-00163 543 45829 84.39963167587477 11.204856826968355 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 125958 144.44724770642202 15.3676629312227 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 17107 16.72238514173998 2.6471679432887645 ERCC-00171 505 8259413 16355.273267326733 2423.447886533417 GL000008.2 209709 965596 4.604456651836593 4.562643071631048 GL000009.2 201709 1068738 5.298415043453688 5.233077569643575 GL000194.1 191469 9755581 50.95122970298064 50.479624733929846 GL000195.1 182896 1132953 6.194520383168577 7.895654222755889 GL000205.2 185591 2971738 16.012295854863652 30.757300392871667 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 156266 0.9514548919562346 1.0073884426650515 GL000214.1 137718 1579190 11.466838031339403 11.27504318372588 GL000216.2 176608 76820 0.43497463308570394 0.5512057440310639 GL000218.1 161147 11097849 68.86785978020069 68.85758887007515 GL000219.1 179198 2169629 12.107439815176509 14.033847146661707 GL000220.1 161802 747515 4.619936712772401 5.582503470140895 GL000221.1 155397 1557548 10.023024897520544 9.974120162666345 GL000224.1 179693 626547 3.4867635355856934 6.550502813945495 GL000225.1 211173 754819 3.5744105543795843 3.5207500738465294 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 234581 0.598327811233456 0.6277490519835608 KI270448.1 7992 0 0.0 0.0 KI270465.1 1774 0 0.0 0.0 KI270466.1 1233 759 0.6155717761557178 0.6580402813635957 KI270467.1 3920 12640 3.2244897959183674 3.01931947422984 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 420180 2.4002741995372885 2.3447419315506823 KI270707.1 32032 0 0.0 0.0 KI270708.1 127682 61946 0.48515844050061874 0.4854425094946527 KI270709.1 66860 0 0.0 0.0 KI270710.1 40176 1760 0.04380724810832338 0.13824011403244824 KI270711.1 42210 26724 0.6331201137171286 1.2428132817014255 KI270712.1 176043 18476 0.10495163113557483 0.28600442512564644 KI270713.1 40745 340645 8.360412320530127 7.792522996191374 KI270714.1 41717 37095 0.8892058393460699 0.8935815497183559 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 86351 2.1554340771803706 2.1862073506125737 KI270718.1 38054 19785 0.5199190623850318 0.6129156906750749 KI270719.1 176845 1448158 8.188854646724533 8.09782424581929 KI270720.1 39050 8498 0.21761843790012805 0.24122654279760958 KI270721.1 100316 140522 1.4007934925634993 2.2645998693570246 KI270722.1 194050 93233 0.4804586446792064 1.2415271412587983 KI270723.1 38115 6010 0.1576807031352486 0.4740996013696183 KI270724.1 39555 5976 0.15108077360637087 0.2304332198092813 KI270725.1 172810 11611 0.06718939876164574 0.11541403373911402 KI270726.1 43739 99106 2.26584969935298 2.7409650430030688 KI270727.1 448248 7804805 17.411801056557977 17.34999067041886 KI270728.1 1872759 5054703 2.6990675255064853 4.021593908812126 KI270729.1 280839 0 0.0 0.0 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 90011 0.5970720511561882 1.1218160071950565 KI270732.1 41543 486 0.011698721806321161 0.10675815696180384 KI270733.1 179772 492979 2.742245733484636 7.4133857155325815 KI270734.1 165050 2714873 16.4487912753711 40.77723551904215 KI270735.1 42811 17516 0.40914718179907034 0.45649570339793266 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 5257778 33.39713654149093 33.17569966880545 KI270742.1 186739 5601902 29.998564841838075 29.759825238802428 KI270743.1 210658 2217657 10.527285932649129 10.458647270471234 KI270744.1 168472 917297 5.444803884324991 5.427971304546375 KI270745.1 41891 2942 0.07022988231362345 0.4372744096202273 KI270746.1 66486 17066 0.25668561802484735 0.30114455318854993 KI270747.1 198735 2408 0.012116637733665434 0.1294840654064006 KI270748.1 93321 11103 0.11897643617192272 0.32350322204777093 KI270749.1 158759 3019 0.01901624474832923 0.19178913394278366 KI270750.1 148850 955711 6.420631508229762 6.508184306918105 KI270751.1 150742 936537 6.212847116264877 6.18551664405835 KI270752.1 27745 0 0.0 0.0 KI270753.1 62944 263179 4.18116103202847 4.260253467961759 KI270754.1 40191 10142 0.2523450523749098 0.49880428340057553 KI270755.1 36723 27843 0.7581896903847725 2.861188024363015 KI270756.1 79590 0 0.0 0.0 KI270757.1 71251 0 0.0 0.0 SIRVome_isoforms 231019 429480138 1859.0684662300503 2196.3759352585216