BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Cshl-Smarter_HpreCap_0+_Heart01Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Cshl-Smarter_HpreCap_0+_Heart01Rep1/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 5,396,837 number of mapped reads = 5,396,837 (100%) number of secondary alignments = 0 number of mapped bases = 26,725,069,307 bp number of sequenced bases = 3,288,322,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,580,301 duplication rate = 30.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 4.7959 >>>>>>> ACTG content number of A's = 924,784,404 bp (28.12%) number of C's = 702,014,098 bp (21.35%) number of T's = 957,428,667 bp (29.12%) number of G's = 704,095,369 bp (21.41%) number of N's = 0 bp (0%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 110,861,497 number of insertions = 22,113,031 mapped reads with insertion percentage = 85.12% number of deletions = 38,281,175 mapped reads with deletion percentage = 92.37% homopolymer indels = 35.42% >>>>>>> Coverage mean coverageData = 8.5915X std coverageData = 130.8325X There is a 2.71% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.89% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.65% of reference with a coverageData >= 7X There is a 0.6% of reference with a coverageData >= 8X There is a 0.56% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.48% of reference with a coverageData >= 12X There is a 0.45% of reference with a coverageData >= 13X There is a 0.43% of reference with a coverageData >= 14X There is a 0.42% of reference with a coverageData >= 15X There is a 0.4% of reference with a coverageData >= 16X There is a 0.39% of reference with a coverageData >= 17X There is a 0.37% of reference with a coverageData >= 18X There is a 0.36% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.33% of reference with a coverageData >= 22X There is a 0.32% of reference with a coverageData >= 23X There is a 0.31% of reference with a coverageData >= 24X There is a 0.3% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.29% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 2877313592 11.55749897465991 103.95049042364934 chr10 133797422 1033979725 7.727949534035118 59.77188534422097 chr11 135086622 1046146883 7.744267104406534 52.661815630739625 chr12 133275309 1987231802 14.910727402627893 185.58096260293448 chr13 114364328 423114675 3.699708487772516 21.592272107797566 chr14 107043718 864051246 8.071947258035264 136.0024901457 chr15 101991189 1141495707 11.192101182387432 134.85754414116735 chr16 90338345 589646916 6.52709451340956 55.3288146203019 chr17 83257441 755481959 9.074047315482588 44.86444224668097 chr18 80373285 650610173 8.094856058203916 182.37033180332267 chr19 58617616 1000607911 17.070088810844847 117.08224007081233 chr2 242193529 2070645539 8.549549393617367 56.78202998846074 chr20 64444167 350406490 5.43736549500283 26.283778010022925 chr21 46709983 361544882 7.74020581424746 44.38024410140095 chr22 50818468 377274504 7.423964531949291 42.75897202241312 chr3 198295559 1406166670 7.091266577482958 55.41824879431754 chr4 190214555 1497489525 7.87263374771715 44.07816631996194 chr5 181538259 1570621443 8.651737940265253 41.20541222336279 chr6 170805979 1597922832 9.355192607162774 34.66242794208196 chr7 159345973 1221728364 7.667143015907907 51.44833835465078 chr8 145138636 1172384114 8.077684525021994 33.911491233060346 chr9 138394717 578103239 4.1772059767281435 22.685440689895163 chrIS 10567884 0 0.0 0.0 chrM 16569 572226025 34535.942120828055 36509.30440106265 chrX 156040895 720502227 4.617393581342891 40.9213597029553 chrY 57227415 72826090 1.2725734685028145 8.926410517579656 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 1665 0.007939573408866573 0.08765918140406148 GL000009.2 201709 5407 0.026805943215225895 0.16296432322895865 GL000194.1 191469 2685680 14.0267092845317 14.225326119187384 GL000195.1 182896 297343 1.6257490595748403 1.8974263277401244 GL000205.2 185591 310380 1.672387130841474 2.2125265745489147 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 1505 0.009163475179464073 0.09522369295823783 GL000214.1 137718 39815 0.2891052730942941 0.4323761803947585 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 1152307 7.150657474231602 8.037463625831379 GL000219.1 179198 367857 2.0527963481735285 2.182302163081463 GL000220.1 161802 7332 0.04531464382393296 0.14209419285233899 GL000221.1 155397 84777 0.5455510724145254 0.5679377515443912 GL000224.1 179693 1020 0.005676347993522285 0.07439146249184829 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 0 0.0 0.0 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 1934 0.4933673469387755 0.4966657884896643 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 73719 0.4211190768615578 0.4295315795996272 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 32574 0.7717128642501777 1.3348157330611887 KI270712.1 176043 6999 0.03975733201547349 0.9742390430183476 KI270713.1 40745 1182 0.02900969444103571 0.1672817403876428 KI270714.1 41717 232 0.005561281971378574 0.0735651547718388 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 3893 0.09717437971144725 0.5246451434051965 KI270718.1 38054 652 0.017133547064697534 0.12976898177021862 KI270719.1 176845 1349 0.0076281489439905 0.0864598027252174 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 47165 0.47016428087244305 4.298151110158164 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 2487 0.005548267923113991 0.08984331774476544 KI270728.1 1872759 123238 0.06580558416753036 0.24564321858226745 KI270729.1 280839 46467 0.16545778898229946 0.16899809697842047 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 633 0.004198893561696539 0.093834788990081 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 241911 1.3456544956945464 1.3342674963250092 KI270734.1 165050 969044 5.87121478339897 15.200564513607207 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 104824 0.665836678693023 0.6643681578177918 KI270742.1 186739 1829437 9.796759112986575 9.667585163229827 KI270743.1 210658 724 0.0034368502501685196 0.05803848290358172 KI270744.1 168472 21782 0.12929151431691913 0.6604106151622919 KI270745.1 41891 1466 0.03499558377694493 0.20430813663276942 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 1478 0.009804832097225723 0.07982647823267651 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 777078496 3363.6995052355 3718.373626119256