BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-CapTrap_Hv3_0+_Brain01Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-CapTrap_Hv3_0+_Brain01Rep1/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 7,090,592 number of mapped reads = 7,090,592 (100%) number of secondary alignments = 0 number of mapped bases = 76,611,688,598 bp number of sequenced bases = 4,323,125,021 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,338,098 duplication rate = 41.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 2.1497 >>>>>>> ACTG content number of A's = 1,085,065,933 bp (25.1%) number of C's = 1,049,427,971 bp (24.27%) number of T's = 1,133,026,678 bp (26.21%) number of G's = 1,055,604,439 bp (24.42%) number of N's = 0 bp (0%) GC percentage = 48.69% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 183,265,891 number of insertions = 32,137,246 mapped reads with insertion percentage = 91.63% number of deletions = 62,279,462 mapped reads with deletion percentage = 97.46% homopolymer indels = 35.12% >>>>>>> Coverage mean coverageData = 24.629X std coverageData = 110.5625X There is a 1.71% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.55% of reference with a coverageData >= 6X There is a 0.5% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 6894331030 27.69292302088114 95.3747643470483 chr10 133797422 2673448698 19.98131696438815 84.21587479413729 chr11 135086622 2698768542 19.978059278142286 122.41990534055356 chr12 133275309 2977046306 22.337568213779193 210.86095976111767 chr13 114364328 1398363271 12.227267850513668 53.56639934218232 chr14 107043718 1940626236 18.129286540663696 73.84926657179604 chr15 101991189 1914397689 18.77022621042294 128.4363757259518 chr16 90338345 1503244955 16.640164871295795 74.92426516381228 chr17 83257441 3111610543 37.37336273643097 150.5870937257889 chr18 80373285 1183775099 14.728464800213155 86.52724012460159 chr19 58617616 3107211796 53.008157070052114 217.6503641229883 chr2 242193529 7150655662 29.524552912394284 141.12642464706684 chr20 64444167 1145260248 17.771356219097378 67.95084673538604 chr21 46709983 2271653137 48.633139879327295 74.13657107265726 chr22 50818468 2114113973 41.60129291973146 133.42311835399417 chr3 198295559 4752452781 23.966511428528765 97.68443819565256 chr4 190214555 2403526784 12.635872076140545 72.48166799342643 chr5 181538259 6982801892 38.46462960736007 93.46575284708868 chr6 170805979 3710783686 21.725139293865116 81.1671325234147 chr7 159345973 5941771319 37.28849375440445 129.7768813269526 chr8 145138636 2925179360 20.15438094650414 62.78462069851577 chr9 138394717 3117427678 22.525626306963726 118.69899381116613 chrIS 10567884 0 0.0 0.0 chrM 16569 13069121 788.7694489709698 941.6858756027934 chrX 156040895 2878460521 18.446834216120074 97.13405424295746 chrY 57227415 826045623 14.434438861164706 31.980168884142078 ERCC-00002 1061 0 0.0 0.0 ERCC-00003 1023 0 0.0 0.0 ERCC-00004 523 0 0.0 0.0 ERCC-00009 984 0 0.0 0.0 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 0 0.0 0.0 ERCC-00022 751 0 0.0 0.0 ERCC-00024 536 0 0.0 0.0 ERCC-00025 1994 0 0.0 0.0 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 0 0.0 0.0 ERCC-00035 1130 0 0.0 0.0 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 0 0.0 0.0 ERCC-00043 1023 0 0.0 0.0 ERCC-00044 1156 0 0.0 0.0 ERCC-00046 522 0 0.0 0.0 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 0 0.0 0.0 ERCC-00060 523 0 0.0 0.0 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 0 0.0 0.0 ERCC-00067 644 0 0.0 0.0 ERCC-00069 1137 0 0.0 0.0 ERCC-00071 642 0 0.0 0.0 ERCC-00073 603 0 0.0 0.0 ERCC-00074 522 0 0.0 0.0 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 0 0.0 0.0 ERCC-00077 273 0 0.0 0.0 ERCC-00078 993 0 0.0 0.0 ERCC-00079 644 0 0.0 0.0 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 0 0.0 0.0 ERCC-00095 521 0 0.0 0.0 ERCC-00096 1107 0 0.0 0.0 ERCC-00097 523 0 0.0 0.0 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 0 0.0 0.0 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 0 0.0 0.0 ERCC-00109 536 0 0.0 0.0 ERCC-00111 994 0 0.0 0.0 ERCC-00112 1136 0 0.0 0.0 ERCC-00113 840 0 0.0 0.0 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 0 0.0 0.0 ERCC-00130 1059 0 0.0 0.0 ERCC-00131 771 0 0.0 0.0 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 0 0.0 0.0 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 0 0.0 0.0 ERCC-00144 538 0 0.0 0.0 ERCC-00145 1042 0 0.0 0.0 ERCC-00147 1023 0 0.0 0.0 ERCC-00148 494 0 0.0 0.0 ERCC-00150 743 0 0.0 0.0 ERCC-00154 537 0 0.0 0.0 ERCC-00156 494 0 0.0 0.0 ERCC-00157 1019 0 0.0 0.0 ERCC-00158 1027 0 0.0 0.0 ERCC-00160 743 0 0.0 0.0 ERCC-00162 523 0 0.0 0.0 ERCC-00163 543 0 0.0 0.0 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 0 0.0 0.0 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 0 0.0 0.0 ERCC-00171 505 0 0.0 0.0 GL000008.2 209709 9352609 44.59803346542113 44.48582767505789 GL000009.2 201709 385843 1.912869529867284 1.9133478203735148 GL000194.1 191469 403028061 2104.9259201228397 2100.129673250339 GL000195.1 182896 56559284 309.2428702650687 306.6884645312038 GL000205.2 185591 5451390 29.373137706031002 40.506870935634375 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 31204 0.18999141495016408 0.21484648225455336 GL000214.1 137718 883339 6.414114349612977 6.357152339387946 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 108261600 671.8188982730054 670.0468334063704 GL000219.1 179198 81061018 452.3544794026719 571.1432459752974 GL000220.1 161802 399618 2.4697964178440315 8.843696959411385 GL000221.1 155397 5618479 36.155646505402295 36.02957762675446 GL000224.1 179693 48879 0.2720139348778194 0.517816764734129 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 182515 0.46552704808690487 0.4725279314423936 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 1403287 8.016263460055411 7.911965121944326 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 8436 0.19985785358919686 1.442725995787373 KI270712.1 176043 493905 2.8055929517220224 7.881068261662704 KI270713.1 40745 327299 8.032862927966622 8.018468169503942 KI270714.1 41717 29036 0.6960232039696047 0.7453607354932295 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 6587 0.16442014876940741 0.21433917578458142 KI270718.1 38054 46218 1.2145372365585747 1.6290973565453897 KI270719.1 176845 1294 0.007317142130113942 0.10723302368442918 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 196212 1.9559392320267954 2.0596868607183416 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 8922 0.05162895665760083 0.06632296038823274 KI270726.1 43739 0 0.0 0.0 KI270727.1 448248 119671 0.2669749781371027 0.34891954689431004 KI270728.1 1872759 859548 0.4589741659231113 1.5195536854956866 KI270729.1 280839 0 0.0 0.0 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 211107 1.400340952810539 4.282269471735649 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 125321 0.6971107847718221 4.046101453506101 KI270734.1 165050 581246 3.5216358679188127 6.494217990868271 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 20718 0.13159967478022258 0.222831906347739 KI270742.1 186739 147832401 791.6525257177129 788.880386874045 KI270743.1 210658 151004273 716.8219246361401 715.2131725276345 KI270744.1 168472 193320 1.147490384158792 1.3108303927319904 KI270745.1 41891 10921 0.2607003891050584 0.547148459836027 KI270746.1 66486 4276 0.0643142917305899 0.09177155954649935 KI270747.1 198735 0 0.0 0.0 KI270748.1 93321 55967 0.5997256780360262 0.7643963521475678 KI270749.1 158759 313 0.001971541770860235 0.043211925397438865 KI270750.1 148850 27681 0.1859657373194491 0.19078162583989008 KI270751.1 150742 753409 4.998003210783988 4.970632047264165 KI270752.1 27745 0 0.0 0.0 KI270753.1 62944 0 0.0 0.0 KI270754.1 40191 6841 0.17021223657037646 0.6284144927521385 KI270755.1 36723 646 0.017591155406693353 0.1301543686256971 KI270756.1 79590 0 0.0 0.0 KI270757.1 71251 0 0.0 0.0 SIRVome_isoforms 231019 69954 0.3028062626883503 0.37949208904385456