BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Cshl-Smarter_HpreCap_0+_Brain01Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Cshl-Smarter_HpreCap_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 = 6,556,308 number of mapped reads = 6,556,308 (100%) number of secondary alignments = 0 number of mapped bases = 29,046,575,872 bp number of sequenced bases = 4,314,273,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,105,903 duplication rate = 26.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 5.8952 >>>>>>> ACTG content number of A's = 1,260,527,842 bp (29.22%) number of C's = 874,740,804 bp (20.28%) number of T's = 1,299,347,206 bp (30.12%) number of G's = 879,657,970 bp (20.39%) number of N's = 0 bp (0%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 133,417,423 number of insertions = 27,661,305 mapped reads with insertion percentage = 83.85% number of deletions = 45,217,168 mapped reads with deletion percentage = 91.1% homopolymer indels = 36.69% >>>>>>> Coverage mean coverageData = 9.3378X std coverageData = 114.9601X There is a 7.42% of reference with a coverageData >= 1X There is a 3.52% of reference with a coverageData >= 2X There is a 2.38% of reference with a coverageData >= 3X There is a 1.84% of reference with a coverageData >= 4X There is a 1.52% of reference with a coverageData >= 5X There is a 1.32% of reference with a coverageData >= 6X There is a 1.17% of reference with a coverageData >= 7X There is a 1.06% of reference with a coverageData >= 8X There is a 0.97% of reference with a coverageData >= 9X There is a 0.9% of reference with a coverageData >= 10X There is a 0.84% of reference with a coverageData >= 11X There is a 0.79% of reference with a coverageData >= 12X There is a 0.75% of reference with a coverageData >= 13X There is a 0.71% of reference with a coverageData >= 14X There is a 0.67% of reference with a coverageData >= 15X There is a 0.65% of reference with a coverageData >= 16X There is a 0.62% of reference with a coverageData >= 17X There is a 0.59% of reference with a coverageData >= 18X There is a 0.57% of reference with a coverageData >= 19X There is a 0.55% of reference with a coverageData >= 20X There is a 0.53% of reference with a coverageData >= 21X There is a 0.52% of reference with a coverageData >= 22X There is a 0.5% of reference with a coverageData >= 23X There is a 0.49% of reference with a coverageData >= 24X There is a 0.47% of reference with a coverageData >= 25X There is a 0.46% of reference with a coverageData >= 26X There is a 0.45% of reference with a coverageData >= 27X There is a 0.44% of reference with a coverageData >= 28X There is a 0.43% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.41% of reference with a coverageData >= 31X There is a 0.4% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.38% 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 0.34% of reference with a coverageData >= 39X There is a 0.34% of reference with a coverageData >= 40X There is a 0.33% of reference with a coverageData >= 41X There is a 0.32% of reference with a coverageData >= 42X There is a 0.32% of reference with a coverageData >= 43X There is a 0.31% of reference with a coverageData >= 44X There is a 0.31% of reference with a coverageData >= 45X There is a 0.3% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.29% of reference with a coverageData >= 48X There is a 0.29% of reference with a coverageData >= 49X There is a 0.29% of reference with a coverageData >= 50X There is a 0.28% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 2170737693 8.71934805120231 49.48643954157165 chr10 133797422 943314507 7.050319003904275 37.5176363638163 chr11 135086622 1073306045 7.945317079584683 42.29158597155301 chr12 133275309 1443609813 10.831787401820993 81.06472938644772 chr13 114364328 570268031 4.986415265781127 45.399807671842666 chr14 107043718 930677832 8.694371322191929 57.026712089258005 chr15 101991189 712035420 6.981342476554519 38.47117466289677 chr16 90338345 883632884 9.781371177433016 40.05905082692626 chr17 83257441 967337544 11.6186317088463 58.82794959726505 chr18 80373285 1703750428 21.197969300371387 197.04623809030738 chr19 58617616 727276606 12.407133821341352 107.10315975100758 chr2 242193529 2651213539 10.946673719759044 74.10260645772087 chr20 64444167 794645673 12.330761805021082 52.03741071073314 chr21 46709983 325965450 6.978496438330967 34.446615725767664 chr22 50818468 403653709 7.943051510328883 42.920342266131485 chr3 198295559 1943850967 9.802796274423876 48.88295213440502 chr4 190214555 1342402125 7.057304973323413 51.35031999386552 chr5 181538259 1653676789 9.109246712562117 44.57863469229639 chr6 170805979 1108595581 6.490379244862383 42.62972723019133 chr7 159345973 1264462137 7.93532533765381 47.49060939992294 chr8 145138636 1309704752 9.023818799013656 57.69609386507759 chr9 138394717 718991242 5.195221736679443 25.0231749580452 chrIS 10567884 0 0.0 0.0 chrM 16569 419009081 25288.73685798781 29869.634050670047 chrX 156040895 1019538918 6.533793067516051 44.72892358283042 chrY 57227415 39972493 0.6984850355376003 2.7574809437423853 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 209450 0.9987649552475096 0.9877859480394189 GL000009.2 201709 572 0.0028357683593691905 0.05289753925988611 GL000194.1 191469 1351796 7.060129838250578 7.022098357362968 GL000195.1 182896 635982 3.4772876388767386 3.7579826967066703 GL000205.2 185591 70099 0.37770689311442907 0.5531407062281111 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 1877 0.013629300454552056 0.13661995526884563 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 324596 2.0142850937342924 2.1707148554620126 GL000219.1 179198 1271379 7.094828067277537 7.887038576740836 GL000220.1 161802 200409 1.2386064449141543 1.2146139472800868 GL000221.1 155397 152778 0.9831463927875056 1.0652411532430242 GL000224.1 179693 28461 0.1583868041604292 0.20758543651043104 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 467 0.28268765133171914 0.4494286073280078 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 60681 0.15477438459831505 0.18070025229669784 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 28603 0.1633943617720145 0.5551423797015146 KI270707.1 32032 7659 0.23910464535464535 0.6256615075802612 KI270708.1 127682 0 0.0 0.0 KI270709.1 66860 194 0.0029015854023332335 0.053788160448989146 KI270710.1 40176 0 0.0 0.0 KI270711.1 42210 112151 2.6569770196635867 4.978419610703857 KI270712.1 176043 37486 0.212936612077731 2.578364702321997 KI270713.1 40745 26534 0.6512210087127255 1.2208203735850913 KI270714.1 41717 14553 0.34885058848910516 0.6161550810113323 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 10780 0.26908292147171886 1.4297032776537053 KI270718.1 38054 43573 1.1450307457823095 1.675239937637453 KI270719.1 176845 734 0.004150527297916254 0.07478481388785425 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 447 0.004455919295027712 0.06645528387193009 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 555 0.0032116196979341473 0.036269249279745355 KI270726.1 43739 0 0.0 0.0 KI270727.1 448248 20532 0.04580500080312684 0.34802517629230756 KI270728.1 1872759 16603 0.008865529414089052 0.13247435662165366 KI270729.1 280839 585 0.002083044021663658 0.07845883539631184 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 3816 0.025312761187099513 0.16593518196178694 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 526374 2.9280088111608036 2.8698591388812447 KI270734.1 165050 986754 5.978515601332929 13.942794856472487 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 5122 0.03253468164032725 0.25249196042242195 KI270742.1 186739 81432 0.4360738785149326 0.5256926700063229 KI270743.1 210658 1384009 6.5699332567479045 6.5484752010332405 KI270744.1 168472 29455 0.17483617455719644 1.1051005820576039 KI270745.1 41891 16923 0.4039769878971617 0.9606467447208134 KI270746.1 66486 974 0.01464970068886683 0.062166168661446565 KI270747.1 198735 0 0.0 0.0 KI270748.1 93321 10150 0.1087643724349289 0.166212265919439 KI270749.1 158759 0 0.0 0.0 KI270750.1 148850 0 0.0 0.0 KI270751.1 150742 1390 0.00922105319021905 0.09517293344206865 KI270752.1 27745 176 0.006343485312668949 0.07757940080617903 KI270753.1 62944 0 0.0 0.0 KI270754.1 40191 0 0.0 0.0 KI270755.1 36723 898 0.024453339868747107 0.15403206953961282 KI270756.1 79590 0 0.0 0.0 KI270757.1 71251 0 0.0 0.0 SIRVome_isoforms 231019 1917269604 8299.185798570681 8917.89853235489