BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-Smarter_Hv3_0+_Brain01Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-Smarter_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 = 2,619,538 number of mapped reads = 2,619,538 (100%) number of secondary alignments = 0 number of mapped bases = 11,986,033,077 bp number of sequenced bases = 1,340,786,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,768,732 duplication rate = 23.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 3.9363 >>>>>>> ACTG content number of A's = 371,969,506 bp (27.74%) number of C's = 291,144,956 bp (21.71%) number of T's = 385,139,279 bp (28.72%) number of G's = 292,532,366 bp (21.82%) number of N's = 0 bp (0%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 52,989,452 number of insertions = 8,702,315 mapped reads with insertion percentage = 81.73% number of deletions = 17,380,352 mapped reads with deletion percentage = 92.9% homopolymer indels = 36.77% >>>>>>> Coverage mean coverageData = 3.8532X std coverageData = 30.2283X There is a 3.85% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 1.09% of reference with a coverageData >= 3X There is a 0.84% of reference with a coverageData >= 4X There is a 0.69% of reference with a coverageData >= 5X There is a 0.6% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 1012825354 4.06828370147447 24.395017571851362 chr10 133797422 423655888 3.1663979893424257 24.056236680276587 chr11 135086622 432097118 3.1986669856915957 30.919469177043663 chr12 133275309 543541595 4.078336783297197 39.434757791554986 chr13 114364328 220541389 1.928410657910743 9.5288563298474 chr14 107043718 353386248 3.301326360879954 15.424403778155108 chr15 101991189 284364581 2.7881288941537883 16.70377332910998 chr16 90338345 305451815 3.3811978180472533 12.359076309501186 chr17 83257441 556591261 6.685183381987443 32.963490940726174 chr18 80373285 237136219 2.950435819563677 26.999398970154726 chr19 58617616 378779055 6.461863870410561 31.027816639865584 chr2 242193529 1090873150 4.504138300078199 16.996624674056328 chr20 64444167 210335912 3.2638471686661727 12.153670652808419 chr21 46709983 248172347 5.313047255872476 13.009831314828249 chr22 50818468 301415393 5.931217623482865 40.570284933329404 chr3 198295559 740382006 3.733729639401556 19.659476618258978 chr4 190214555 418064213 2.197856063117778 16.073582566832236 chr5 181538259 1120452862 6.171992990193874 20.649630043962965 chr6 170805979 545369783 3.19291974550844 16.17843664068132 chr7 159345973 838703092 5.263409399119236 25.942197173910824 chr8 145138636 485660924 3.346186359364711 13.813432223164911 chr9 138394717 445005255 3.2154786298670635 25.844392287788352 chrIS 10567884 0 0.0 0.0 chrM 16569 100508168 6066.037057154927 6708.78468477462 chrX 156040895 396798776 2.5429152787158777 12.245016813493452 chrY 57227415 61758204 1.0791716522579258 3.352776503062307 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 976558 4.656729086496049 4.613430053478429 GL000009.2 201709 0 0.0 0.0 GL000194.1 191469 21789549 113.80196794259123 113.5989845113293 GL000195.1 182896 10428859 57.02070575627679 57.303718800220295 GL000205.2 185591 364021 1.961415154829706 2.515105780712684 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 2394 0.01738334858188472 0.13624988111642455 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 7466011 46.330437426697365 46.591061296326686 GL000219.1 179198 4694717 26.198489938503776 38.41799560015297 GL000220.1 161802 11430 0.07064189565023918 0.46473411389410846 GL000221.1 155397 363050 2.3362741880473883 2.3428956178037206 GL000224.1 179693 1716 0.009549620742043375 0.16475565489899455 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 158 0.09564164648910412 0.2932657224902217 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 752 0.0019180688719357447 0.04334533583146576 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 287807 1.6440947130901717 1.6628981352695886 KI270707.1 32032 2151 0.0671515984015984 0.29487443112978473 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 111423 2.639729921819474 5.807350346945948 KI270712.1 176043 33477 0.1901637668069733 0.5905852077092147 KI270713.1 40745 45266 1.110958399803657 1.6811205579792947 KI270714.1 41717 4841 0.11604381906656759 0.3040447555368224 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 1533 0.00996755505562455 0.03484993205581585 KI270717.1 40062 3558 0.08881234087164895 0.3644852191197476 KI270718.1 38054 65452 1.719976874967152 2.139539360284742 KI270719.1 176845 30140 0.1704317340043541 0.18063447713461217 KI270720.1 39050 1362 0.03487836107554417 0.07483128114549989 KI270721.1 100316 3780 0.0376809282666773 0.2351590508443566 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 5665 0.012638093198408024 0.11895049172845006 KI270728.1 1872759 39444 0.021061973270452845 0.33667694796398634 KI270729.1 280839 0 0.0 0.0 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 70618 0.4684320150709102 1.1635158412950322 KI270732.1 41543 965 0.023228943504320823 0.17259241999283553 KI270733.1 179772 12783 0.07110673519791737 0.5125992788551903 KI270734.1 165050 236363 1.4320690699787944 2.6531756032948626 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 3235 0.020548554296458153 0.1910207628229903 KI270742.1 186739 2640733 14.141304173204311 14.067673525837813 KI270743.1 210658 4977358 23.627671391544588 23.583250302797055 KI270744.1 168472 225387 1.3378306187378317 2.099605321556626 KI270745.1 41891 61323 1.4638705211143206 1.4429695568063314 KI270746.1 66486 0 0.0 0.0 KI270747.1 198735 0 0.0 0.0 KI270748.1 93321 37216 0.3987955551269275 0.622590094334031 KI270749.1 158759 0 0.0 0.0 KI270750.1 148850 0 0.0 0.0 KI270751.1 150742 11975 0.07944036831141951 0.19922695922887426 KI270752.1 27745 0 0.0 0.0 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 179149399 775.4747401728862 902.344366674676