BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-dRNA_HpreCap_0+_Heart02Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-dRNA_HpreCap_0+_Heart02Rep1/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 1,545,314 number of mapped reads = 1,545,314 (100%) number of secondary alignments = 0 number of mapped bases = 7,566,516,410 bp number of sequenced bases = 1,128,733,640 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,270,864 duplication rate = 27.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 3.6621 >>>>>>> ACTG content number of A's = 298,478,383 bp (26.44%) number of C's = 314,645,643 bp (27.88%) number of T's = 256,225,848 bp (22.7%) number of G's = 259,383,766 bp (22.98%) number of N's = 0 bp (0%) GC percentage = 50.86% >>>>>>> Mismatches and indels general error rate = 0.0169 number of mismatches = 97,041,042 number of insertions = 20,327,339 mapped reads with insertion percentage = 99.58% number of deletions = 37,589,524 mapped reads with deletion percentage = 99.98% homopolymer indels = 35.66% >>>>>>> Coverage mean coverageData = 2.4325X std coverageData = 73.7573X There is a 0.97% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.11% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.1% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 705160887 2.8324671496122322 45.2996150165213 chr10 133797422 301259249 2.2516072768576962 9.19539239869598 chr11 135086622 375880490 2.782514540929153 27.417469678504425 chr12 133275309 658986648 4.944551642345095 97.13545641685947 chr13 114364328 72300981 0.6321987132211366 5.692489765981344 chr14 107043718 207863258 1.9418538694629421 40.702985121191915 chr15 101991189 556681824 5.458136427843781 72.55098935401502 chr16 90338345 206954704 2.290884385805385 19.566225135545256 chr17 83257441 264413442 3.175853579261462 23.465790060465988 chr18 80373285 104101365 1.295223468842912 14.011726226806923 chr19 58617616 599515654 10.22756800617753 62.281077081488796 chr2 242193529 530684633 2.1911594219348447 39.99107987896084 chr20 64444167 165234353 2.5639923780844276 19.207313054063768 chr21 46709983 60519485 1.2956434816086317 6.533937058525862 chr22 50818468 312386809 6.147111892471847 69.55109124057654 chr3 198295559 365063690 1.841007896702316 27.148564783479845 chr4 190214555 240292567 1.2632711886847985 6.60586022439085 chr5 181538259 315794598 1.739548455182662 8.251275516361847 chr6 170805979 238209829 1.3946223100304938 8.080999848743595 chr7 159345973 259032555 1.6255983764333974 11.018280555218894 chr8 145138636 281570007 1.9400072562346529 8.566062159608402 chr9 138394717 225458915 1.6291005891503791 12.684405651504438 chrIS 10567884 0 0.0 0.0 chrM 16569 349916438 21118.742108757317 20263.25488206958 chrX 156040895 155061763 0.9937251577543181 8.039340440196547 chrY 57227415 11855828 0.20717042697105925 1.1022315177723483 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 0 0.0 0.0 GL000009.2 201709 0 0.0 0.0 GL000194.1 191469 240690 1.2570703351456372 1.2724370004875216 GL000195.1 182896 42925 0.23469622080307934 0.24370169119909288 GL000205.2 185591 5434 0.02927943704166689 0.13952464285049399 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 0 0.0 0.0 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 275374 1.7088372728006107 1.7056153408277517 GL000219.1 179198 22988 0.12828268172635857 0.16216904126872264 GL000220.1 161802 118778 0.7340947577903858 5.118043035832775 GL000221.1 155397 426 0.002741365663429796 0.05073316827686047 GL000224.1 179693 0 0.0 0.0 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 465 0.0011860399274602677 0.03363327517782927 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 135831 0.7759332781125932 0.7748233149574741 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 529 0.012532575219142384 0.10808604132522616 KI270712.1 176043 0 0.0 0.0 KI270713.1 40745 0 0.0 0.0 KI270714.1 41717 0 0.0 0.0 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 0 0.0 0.0 KI270718.1 38054 0 0.0 0.0 KI270719.1 176845 0 0.0 0.0 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 349501 3.4840005582359743 17.975269970062897 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 0 0.0 0.0 KI270728.1 1872759 28555 0.015247557213715165 0.06110686566227985 KI270729.1 280839 0 0.0 0.0 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 0 0.0 0.0 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 314035 1.7468515675411076 6.160905509681447 KI270734.1 165050 567883 3.4406725234777342 6.6626650699535395 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 17422 0.11066365160831343 0.12103818852929474 KI270742.1 186739 191454 1.025249144527924 1.0216915559308999 KI270743.1 210658 0 0.0 0.0 KI270744.1 168472 3857 0.02289401206135144 0.17310866810975123 KI270745.1 41891 291 0.0069465995082475945 0.08002504572054854 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 0 0.0 0.0 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 0 0.0 0.0