BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-Telop_HpreCap_0+_Brain01Rep3.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-Telop_HpreCap_0+_Brain01Rep3/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 8,011,206 number of mapped reads = 8,011,206 (100%) number of secondary alignments = 0 number of mapped bases = 68,123,400,877 bp number of sequenced bases = 6,011,411,188 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,362,649 duplication rate = 42.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.994 >>>>>>> ACTG content number of A's = 1,629,817,203 bp (27.11%) number of C's = 1,380,762,408 bp (22.97%) number of T's = 1,649,357,086 bp (27.44%) number of G's = 1,351,474,491 bp (22.48%) number of N's = 0 bp (0%) GC percentage = 45.45% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 238,430,390 number of insertions = 47,573,857 mapped reads with insertion percentage = 93.22% number of deletions = 81,200,946 mapped reads with deletion percentage = 97.32% homopolymer indels = 35.32% >>>>>>> Coverage mean coverageData = 21.9002X std coverageData = 346.9719X There is a 2.07% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 1.39% of reference with a coverageData >= 3X There is a 1.19% of reference with a coverageData >= 4X There is a 1.03% of reference with a coverageData >= 5X There is a 0.91% of reference with a coverageData >= 6X There is a 0.81% of reference with a coverageData >= 7X There is a 0.74% of reference with a coverageData >= 8X There is a 0.68% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.59% of reference with a coverageData >= 11X There is a 0.56% of reference with a coverageData >= 12X There is a 0.53% of reference with a coverageData >= 13X There is a 0.51% of reference with a coverageData >= 14X There is a 0.48% of reference with a coverageData >= 15X There is a 0.46% of reference with a coverageData >= 16X There is a 0.45% of reference with a coverageData >= 17X There is a 0.43% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.4% of reference with a coverageData >= 20X There is a 0.39% of reference with a coverageData >= 21X There is a 0.38% of reference with a coverageData >= 22X There is a 0.37% of reference with a coverageData >= 23X There is a 0.36% of reference with a coverageData >= 24X There is a 0.35% of reference with a coverageData >= 25X There is a 0.34% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.31% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.29% of reference with a coverageData >= 32X There is a 0.29% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.28% of reference with a coverageData >= 35X There is a 0.27% of reference with a coverageData >= 36X There is a 0.27% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.26% of reference with a coverageData >= 39X There is a 0.25% of reference with a coverageData >= 40X There is a 0.25% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.24% of reference with a coverageData >= 43X There is a 0.24% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.23% of reference with a coverageData >= 46X There is a 0.23% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.22% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 6519564835 26.187574446261923 305.78447828533496 chr10 133797422 1914974977 14.31249532595628 55.12690542473299 chr11 135086622 3019943885 22.355610350520127 152.27177607693508 chr12 133275309 3003498947 22.53604939681663 136.8439075138937 chr13 114364328 976097864 8.534985349627553 48.70530136034493 chr14 107043718 2190989328 20.468172901094487 69.3681238902697 chr15 101991189 2467568776 24.193940674620432 162.48877145620727 chr16 90338345 1407893245 15.584669444630627 56.99976989946536 chr17 83257441 3124851007 37.532393134686906 128.74040270227545 chr18 80373285 1707008236 21.23850276867494 151.39412254097206 chr19 58617616 1925757524 32.85288033549505 158.62348501106163 chr2 242193529 8123205202 33.540141371820056 116.97559828850854 chr20 64444167 4431536440 68.76551666809503 231.9681018753509 chr21 46709983 1358738121 29.088816431382558 125.75409852885679 chr22 50818468 1272239151 25.034976477449103 84.85940727432713 chr3 198295559 5204102156 26.244168967999933 88.10904560650582 chr4 190214555 3249429230 17.082968387986924 100.07351203765391 chr5 181538259 2892330390 15.932346194859123 59.759669916688964 chr6 170805979 2149716161 12.58571961933487 147.51543488873153 chr7 159345973 2661385846 16.70193350917001 117.10418647072386 chr8 145138636 2870031040 19.77441099832301 52.544743528939776 chr9 138394717 1732585259 12.519157497897842 64.55063896793601 chrIS 10567884 0 0.0 0.0 chrM 16569 1370405678 82709.01551089383 115032.76402366335 chrX 156040895 1936349381 12.409242980822432 69.11801864372427 chrY 57227415 138495555 2.4200910525139046 12.425929092065092 ERCC-00002 1061 14739689 13892.261074458058 882.4501442061883 ERCC-00003 1023 1255120 1226.9012707722386 99.8251985838246 ERCC-00004 523 7388385 14126.931166347993 1360.9666526390022 ERCC-00009 984 3593182 3651.607723577236 285.8687742553517 ERCC-00012 994 983 0.9889336016096579 0.1721498180013578 ERCC-00013 808 4182 5.175742574257426 0.7104822799276352 ERCC-00014 1957 13628 6.963719979560552 0.7360966876531793 ERCC-00016 844 4166 4.936018957345971 0.5100074408053077 ERCC-00017 1136 0 0.0 0.0 ERCC-00019 644 103569 160.82142857142858 13.010543212866875 ERCC-00022 751 216037 287.66577896138483 24.68531911580904 ERCC-00024 536 0 0.0 0.0 ERCC-00025 1994 40763 20.44282848545637 2.025583683447461 ERCC-00028 1130 0 0.0 0.0 ERCC-00031 1138 0 0.0 0.0 ERCC-00033 2022 18079 8.941147378832838 0.794472634843893 ERCC-00034 1019 73005 71.64376840039255 5.328173149393232 ERCC-00035 1130 18906 16.730973451327433 1.6483431095062389 ERCC-00039 740 9534 12.883783783783784 1.0327330820206138 ERCC-00040 744 3697 4.969086021505376 0.44123500656784553 ERCC-00041 1122 5578 4.971479500891266 0.33436123172727034 ERCC-00042 1023 2018776 1973.3880742913002 114.88541551243699 ERCC-00043 1023 200774 196.26001955034212 14.011968581306089 ERCC-00044 1156 97862 84.65570934256056 4.960776033945661 ERCC-00046 522 13723474 26290.180076628352 2090.1603332658083 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 158450 578.2846715328467 57.830022689965666 ERCC-00053 1023 107134 104.72531769305962 7.088224116311817 ERCC-00054 274 24647 89.95255474452554 9.011081940641597 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 7883 6.939260563380282 0.705994147505659 ERCC-00059 525 6211 11.83047619047619 1.1463296451408567 ERCC-00060 523 1085192 2074.9369024856596 186.81983898390553 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 429466 419.8103616813294 26.628093079244422 ERCC-00067 644 9352 14.521739130434783 1.3745350034940744 ERCC-00069 1137 0 0.0 0.0 ERCC-00071 642 202877 316.00778816199374 20.373727754647582 ERCC-00073 603 6556 10.872305140961858 1.0265741826848536 ERCC-00074 522 11493096 22017.42528735632 1572.5081867728838 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 958688 1493.2834890965732 115.37648792159065 ERCC-00077 273 6108 22.373626373626372 2.139266269043346 ERCC-00078 993 54074 54.4551863041289 4.457088684016018 ERCC-00079 644 278882 433.04658385093165 31.58334813966705 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 16643 19.71919431279621 1.8692646234481023 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 252110 224.29715302491104 16.94257883847245 ERCC-00095 521 70879 136.04414587332053 12.507830520229266 ERCC-00096 1107 42549730 38436.97380307136 2572.472687625067 ERCC-00097 523 2069 3.956022944550669 0.4723295190350429 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 41677 30.87185185185185 2.338906102396994 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 2093341 2048.278864970646 170.4492595737225 ERCC-00109 536 2677 4.994402985074627 0.3674141774181826 ERCC-00111 994 2849934 2867.1368209255534 175.68739407558272 ERCC-00112 1136 59082 52.00880281690141 3.825357444275369 ERCC-00113 840 12893188 15349.033333333333 1011.2548812054669 ERCC-00116 1991 19942 10.01607232546459 0.7635565541435041 ERCC-00117 1136 0 0.0 0.0 ERCC-00120 536 533 0.9944029850746269 0.09620427674890945 ERCC-00123 1022 0 0.0 0.0 ERCC-00126 1118 7676 6.8658318425760285 0.8387931671740156 ERCC-00130 1059 106204810 100287.82813975449 7510.147213924293 ERCC-00131 771 203444 263.8702983138781 18.931995328256846 ERCC-00134 274 1607 5.864963503649635 0.7139958538998862 ERCC-00136 1033 10161084 9836.480154888673 554.8556324018829 ERCC-00137 537 12621 23.502793296089386 2.5213052411840895 ERCC-00138 1024 0 0.0 0.0 ERCC-00142 493 0 0.0 0.0 ERCC-00143 784 5414 6.905612244897959 0.655944686618749 ERCC-00144 538 34905 64.87918215613382 7.177188406039738 ERCC-00145 1042 1356575 1301.8953934740882 118.90581118827944 ERCC-00147 1023 2019 1.9736070381231672 0.30273059312341416 ERCC-00148 494 63462 128.4655870445344 12.145350195882218 ERCC-00150 743 10907 14.679676985195155 1.1821732327688796 ERCC-00154 537 12343 22.98510242085661 2.1430987673869932 ERCC-00156 494 2934 5.939271255060729 0.4919653081734803 ERCC-00157 1019 42511 41.71835132482826 2.662365298460071 ERCC-00158 1027 0 0.0 0.0 ERCC-00160 743 34203 46.033647375504714 4.715877295656765 ERCC-00162 523 39058 74.68068833652008 6.8469719885724825 ERCC-00163 543 74418 137.04972375690608 9.552904777231406 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 414053 474.83142201834863 35.04665578416131 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 25872 25.29032258064516 1.8660991024212683 ERCC-00171 505 8089223 16018.263366336634 1754.454165822109 GL000008.2 209709 0 0.0 0.0 GL000009.2 201709 229 0.0011352988711460568 0.03278190667591976 GL000194.1 191469 7576924 39.57258877416187 39.530513940563544 GL000195.1 182896 981556 5.366743941912343 5.5463751143480255 GL000205.2 185591 158173 0.8522665430974562 1.4440075322302353 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 1025 0.007442745320146967 0.10560052300983527 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 2715044 16.84824414975147 16.858411233842084 GL000219.1 179198 4251467 23.724969028672195 25.530537379149603 GL000220.1 161802 753402 4.6563206882486 9.217762174458011 GL000221.1 155397 32936 0.21194746359324826 0.22176050332365443 GL000224.1 179693 1833933 10.205923436082653 21.1073721061404 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 34616 0.0882923830730422 0.12237545881874147 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 2787 0.015920710633800805 0.22633354730389968 KI270707.1 32032 0 0.0 0.0 KI270708.1 127682 0 0.0 0.0 KI270709.1 66860 456 0.006820221358061622 0.08203321343410085 KI270710.1 40176 0 0.0 0.0 KI270711.1 42210 62080 1.470741530443023 4.997008621611238 KI270712.1 176043 41855 0.2377544122742739 1.5216060767061845 KI270713.1 40745 17760 0.43588170327647563 1.847859395576502 KI270714.1 41717 16888 0.4048229738475921 0.5612525015270807 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 4871 0.12158654086166441 0.7533894033883541 KI270718.1 38054 4864 0.12781836337835706 0.30540313886782894 KI270719.1 176845 0 0.0 0.0 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 170943 1.70404521711392 2.133392645012682 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 6991 0.01559627706091271 0.3371117100969423 KI270728.1 1872759 6601 0.0035247461098838664 0.05724967842127681 KI270729.1 280839 8390 0.029874768105569383 0.037968073963703365 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 334 0.0022155299361874313 0.04595173996310686 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 630699 3.508327214471664 8.695811384011108 KI270734.1 165050 279291 1.6921599515298393 3.6905647043542684 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 1559 0.015688050314465407 0.2526279732276027 KI270739.1 73985 0 0.0 0.0 KI270740.1 37240 0 0.0 0.0 KI270741.1 157432 502541 3.1921146907871334 3.697914417256794 KI270742.1 186739 2112194 11.310942009971136 11.294605332243902 KI270743.1 210658 0 0.0 0.0 KI270744.1 168472 4529 0.026882805451350966 0.667044564790936 KI270745.1 41891 6068 0.14485211620634503 1.2859819405473847 KI270746.1 66486 0 0.0 0.0 KI270747.1 198735 0 0.0 0.0 KI270748.1 93321 334 0.003579044373720813 0.05845758159775329 KI270749.1 158759 561 0.003533657934353328 0.05811472608156968 KI270750.1 148850 0 0.0 0.0 KI270751.1 150742 876 0.005811253665202797 0.10510359419699951 KI270752.1 27745 150301 5.417228329428726 5.3569822018116104 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 206320616 893.0893822586021 1187.107487020963