BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-Telop_HpreCap_0+_Brain01Rep2.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-Telop_HpreCap_0+_Brain01Rep2/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 7,816,321 number of mapped reads = 7,816,321 (100%) number of secondary alignments = 0 number of mapped bases = 140,224,096,253 bp number of sequenced bases = 8,523,607,308 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,353,796 duplication rate = 43.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.1287 >>>>>>> ACTG content number of A's = 2,110,865,778 bp (24.76%) number of C's = 2,138,192,987 bp (25.09%) number of T's = 2,115,887,176 bp (24.82%) number of G's = 2,158,661,367 bp (25.33%) number of N's = 0 bp (0%) GC percentage = 50.41% >>>>>>> Mismatches and indels general error rate = 0.0151 number of mismatches = 1,457,091,611 number of insertions = 117,984,261 mapped reads with insertion percentage = 98.65% number of deletions = 182,155,389 mapped reads with deletion percentage = 99.44% homopolymer indels = 37.22% >>>>>>> Coverage mean coverageData = 45.079X std coverageData = 237.1288X There is a 1.25% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.76% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.64% of reference with a coverageData >= 8X There is a 0.62% of reference with a coverageData >= 9X There is a 0.59% of reference with a coverageData >= 10X There is a 0.57% of reference with a coverageData >= 11X There is a 0.56% of reference with a coverageData >= 12X There is a 0.54% of reference with a coverageData >= 13X There is a 0.52% of reference with a coverageData >= 14X There is a 0.51% of reference with a coverageData >= 15X There is a 0.5% of reference with a coverageData >= 16X There is a 0.48% of reference with a coverageData >= 17X There is a 0.47% of reference with a coverageData >= 18X There is a 0.46% of reference with a coverageData >= 19X There is a 0.46% of reference with a coverageData >= 20X There is a 0.45% of reference with a coverageData >= 21X There is a 0.44% of reference with a coverageData >= 22X There is a 0.43% of reference with a coverageData >= 23X There is a 0.43% of reference with a coverageData >= 24X There is a 0.42% of reference with a coverageData >= 25X There is a 0.41% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.39% of reference with a coverageData >= 29X There is a 0.39% of reference with a coverageData >= 30X There is a 0.38% of reference with a coverageData >= 31X There is a 0.38% of reference with a coverageData >= 32X There is a 0.37% of reference with a coverageData >= 33X There is a 0.37% of reference with a coverageData >= 34X There is a 0.37% of reference with a coverageData >= 35X There is a 0.36% of reference with a coverageData >= 36X There is a 0.36% of reference with a coverageData >= 37X There is a 0.35% of reference with a coverageData >= 38X There is a 0.35% of reference with a coverageData >= 39X There is a 0.35% of reference with a coverageData >= 40X There is a 0.34% of reference with a coverageData >= 41X There is a 0.34% of reference with a coverageData >= 42X There is a 0.33% of reference with a coverageData >= 43X There is a 0.33% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.33% of reference with a coverageData >= 46X There is a 0.32% 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 0.31% of reference with a coverageData >= 50X There is a 0.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 10554356596 42.39439381081722 154.0471968900842 chr10 133797422 4481996094 33.49837408675931 164.980678152973 chr11 135086622 5950190667 44.04722376579969 457.0897116708121 chr12 133275309 4303139447 32.28759684961601 250.8278417458044 chr13 114364328 1981943607 17.330085715189092 107.26450895622877 chr14 107043718 4594432637 42.92108610240911 133.9589188147054 chr15 101991189 4028718074 39.50064817854021 189.37146619585153 chr16 90338345 5252148097 58.13863533807267 369.9805449671965 chr17 83257441 7274895578 87.37832307384994 354.236537282688 chr18 80373285 7751702356 96.44625519536747 435.04253246310213 chr19 58617616 5134878727 87.59958315261406 278.3965802502999 chr2 242193529 9875236388 40.77415457289117 111.00752239148252 chr20 64444167 11519283757 178.74827611628527 646.5398379215713 chr21 46709983 2113441202 45.24602807070172 80.65200551968539 chr22 50818468 3509706979 69.06361244498751 145.25558065191996 chr3 198295559 5949437076 30.002876040204207 73.11946208111327 chr4 190214555 12118332364 63.70875438002103 170.92543305515426 chr5 181538259 6037731366 33.258726833994814 111.72365359214149 chr6 170805979 4913960289 28.769252211013058 413.24716159017134 chr7 159345973 6376836584 40.018812298444466 101.62368923347732 chr8 145138636 8350271032 57.53306812115831 182.90028801933644 chr9 138394717 3474840785 25.108189534431432 108.05451068297678 chrIS 10567884 0 0.0 0.0 chrM 16569 15555281 938.8183354457119 1068.82083867009 chrX 156040895 4489569205 28.771747335850645 146.45789513953616 chrY 57227415 4497019 0.07858155046842497 4.003401909159507 ERCC-00002 1061 3254182 3067.0895381715363 220.55254479513587 ERCC-00003 1023 173848 169.93939393939394 14.207514254759984 ERCC-00004 523 1242124 2374.998087954111 206.77437822263244 ERCC-00009 984 464248 471.7967479674797 35.18305446332896 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 0 0.0 0.0 ERCC-00017 1136 0 0.0 0.0 ERCC-00019 644 7600 11.801242236024844 1.4512445952877957 ERCC-00022 751 30739 40.93075898801598 4.640418991405923 ERCC-00024 536 0 0.0 0.0 ERCC-00025 1994 9942 4.985957873620863 0.3830831442365135 ERCC-00028 1130 2250 1.991150442477876 0.23064941838552502 ERCC-00031 1138 0 0.0 0.0 ERCC-00033 2022 0 0.0 0.0 ERCC-00034 1019 15158 14.875368007850835 1.1555432973078843 ERCC-00035 1130 7533 6.666371681415929 0.8419966834323713 ERCC-00039 740 0 0.0 0.0 ERCC-00040 744 0 0.0 0.0 ERCC-00041 1122 0 0.0 0.0 ERCC-00042 1023 222961 217.94819159335287 14.152782787972232 ERCC-00043 1023 54807 53.57478005865103 3.6472167996487346 ERCC-00044 1156 14923 12.90916955017301 0.7904742808758511 ERCC-00046 522 1887850 3616.5708812260536 266.2018149394674 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 16601 60.58759124087591 6.0615647758287805 ERCC-00053 1023 22750 22.238514173998045 1.2083084169670488 ERCC-00054 274 6999 25.543795620437955 2.191839057222913 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 0 0.0 0.0 ERCC-00059 525 1033 1.9676190476190476 0.28357932498701355 ERCC-00060 523 192579 368.21988527724665 29.673512031147393 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 71049 69.45161290322581 15.17502653468048 ERCC-00067 644 0 0.0 0.0 ERCC-00069 1137 0 0.0 0.0 ERCC-00071 642 68285 106.36292834890966 6.426016000702746 ERCC-00073 603 0 0.0 0.0 ERCC-00074 522 2408421 4613.833333333333 320.2724370095653 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 194018 302.208722741433 21.974215690662557 ERCC-00077 273 1887 6.912087912087912 0.6311111885929931 ERCC-00078 993 14940 15.045317220543806 1.1655642373633062 ERCC-00079 644 19672 30.546583850931675 2.6234075691053578 ERCC-00081 534 2812 5.265917602996255 0.6684107976619766 ERCC-00083 1022 0 0.0 0.0 ERCC-00084 994 1952 1.9637826961770624 0.362812424653565 ERCC-00085 844 1665 1.9727488151658767 0.3088737801460715 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 14731 13.105871886120996 1.1263004357506237 ERCC-00095 521 23975 46.01727447216891 3.787781796755985 ERCC-00096 1107 9938652 8978.0054200542 561.2078697452464 ERCC-00097 523 523 1.0 0.27998907381030935 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 391 0.2896296296296296 0.4155819625860658 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 342302 334.9334637964775 26.503193891700477 ERCC-00109 536 536 1.0 0.13658959117703826 ERCC-00111 994 989121 995.0915492957746 54.64358032095001 ERCC-00112 1136 5157 4.539612676056338 0.9510126814421772 ERCC-00113 840 2995262 3565.788095238095 224.53552835144978 ERCC-00116 1991 0 0.0 0.0 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 7798 6.974955277280858 0.39295977984678165 ERCC-00130 1059 19942309 18831.264400377713 1317.2323099057428 ERCC-00131 771 6815 8.83916990920882 0.854760681278624 ERCC-00134 274 1046 3.8175182481751824 0.6484858202172646 ERCC-00136 1033 1764104 1707.7483059051308 89.47177033764939 ERCC-00137 537 1073 1.9981378026070764 0.16117423325213948 ERCC-00138 1024 0 0.0 0.0 ERCC-00142 493 0 0.0 0.0 ERCC-00143 784 3106 3.961734693877551 0.36004650539545546 ERCC-00144 538 10570 19.646840148698885 2.3196862190823566 ERCC-00145 1042 201712 193.58157389635318 18.20576771465445 ERCC-00147 1023 0 0.0 0.0 ERCC-00148 494 19769 40.01821862348178 3.5974803869725887 ERCC-00150 743 740 0.9959623149394348 0.08959052081099661 ERCC-00154 537 2118 3.9441340782122905 0.39200471501892314 ERCC-00156 494 494 1.0 0.08998425413316952 ERCC-00157 1019 11902 11.680078508341511 1.3957445423273906 ERCC-00158 1027 0 0.0 0.0 ERCC-00160 743 16800 22.611036339165544 2.1831371447830406 ERCC-00162 523 25225 48.231357552581265 4.398795276074721 ERCC-00163 543 38362 70.64825046040515 4.987787655994484 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 10840 12.431192660550458 0.9590667018730036 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 5056 4.9423264907135875 0.5094271105110146 ERCC-00171 505 1128208 2234.0752475247523 230.18977530216517 GL000008.2 209709 0 0.0 0.0 GL000009.2 201709 0 0.0 0.0 GL000194.1 191469 0 0.0 0.0 GL000195.1 182896 0 0.0 0.0 GL000205.2 185591 0 0.0 0.0 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 24685 0.17924309095397842 0.19032164052878447 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 1453 0.009016612161566769 0.15393522753801658 GL000219.1 179198 0 0.0 0.0 GL000220.1 161802 82691 0.5110629040432133 0.7384819817656049 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 19517 0.049780518847832356 0.057846740536104634 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 0 0.0 0.0 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 463 0.0026300392517737145 0.049874932833557664 KI270713.1 40745 159 0.003902319302981961 0.06096418477097826 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 9743 0.24950064020486556 0.2643319788758168 KI270721.1 100316 180669 1.8009988436540532 2.7172217390436746 KI270722.1 194050 267 0.0013759340376191702 0.03699867177849769 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 19460 0.04341346754475201 1.1340361992763115 KI270728.1 1872759 17745 0.009475324908330437 0.3252038370748809 KI270729.1 280839 50215 0.17880351375699244 0.18101578388827733 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 7474 0.04957745731456545 0.44556374129557946 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 500627 2.7847885098903054 3.0207909529925456 KI270734.1 165050 930709 5.638951832777946 6.626664278165217 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 0 0.0 0.0 KI270742.1 186739 205 0.0010977888925184347 0.03295295330413941 KI270743.1 210658 0 0.0 0.0 KI270744.1 168472 891 0.005288712664419013 0.08137082650819594 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 0 0.0 0.0 KI270752.1 27745 52375130 1887.732204000721 1895.5628330085074 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 64851418 280.71897982417033 374.1053436306837