BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/pacBio-Cshl-Smarter_HpreCap_0+_Heart01Rep1.bam outfile = output/mappings/longReadMapping/bamqc/pacBio-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 = 502,412 number of mapped reads = 502,412 (100%) number of secondary alignments = 0 number of mapped bases = 5,044,712,262 bp number of sequenced bases = 530,737,753 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 367,193 duplication rate = 27.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 4.5894 >>>>>>> ACTG content number of A's = 145,736,287 bp (27.46%) number of C's = 119,056,634 bp (22.43%) number of T's = 147,158,008 bp (27.73%) number of G's = 118,786,824 bp (22.38%) number of N's = 0 bp (0%) GC percentage = 44.81% >>>>>>> Mismatches and indels general error rate = 0.0004 number of mismatches = 852,925 number of insertions = 690,452 mapped reads with insertion percentage = 24.8% number of deletions = 243,409 mapped reads with deletion percentage = 21.9% homopolymer indels = 39.53% >>>>>>> Coverage mean coverageData = 1.6218X std coverageData = 15.3986X There is a 1.22% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.08% of reference with a coverageData >= 29X There is a 0.08% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 569327273 2.2868551388483565 24.151178867713078 chr10 133797422 212016336 1.5846070337588418 5.727921257364472 chr11 135086622 204766855 1.5158189017414323 7.95922177594608 chr12 133275309 348188304 2.612549215699061 26.85612590025476 chr13 114364328 77290910 0.6758305789196786 2.85607013598253 chr14 107043718 145563311 1.3598491692898784 16.089878893584984 chr15 101991189 239844240 2.3516172558788386 24.953300444951118 chr16 90338345 133362712 1.47625808287721 13.618654071947077 chr17 83257441 137998524 1.6574917790230905 7.3094240576322225 chr18 80373285 119604257 1.4881096000990877 23.168613399082286 chr19 58617616 186005025 3.1731932769152538 23.347276608382646 chr2 242193529 443367198 1.8306318910774861 9.005111642703445 chr20 64444167 78353439 1.215834460239047 3.4298804272747154 chr21 46709983 42784197 0.9159540263587764 4.807118134108803 chr22 50818468 76955787 1.5143271733417858 4.988581277979101 chr3 198295559 292703556 1.4760973845107646 9.852987470843127 chr4 190214555 301305119 1.5840276733817766 6.4188565140751965 chr5 181538259 315282478 1.736727452035331 6.090870995307495 chr6 170805979 277622491 1.6253675229951992 6.031530609480432 chr7 159345973 254092798 1.5945981766354396 5.651231922353834 chr8 145138636 198628263 1.3685416128617882 3.9332914773320757 chr9 138394717 102172796 0.7382709269169574 3.015169686847237 chrIS 10567884 0 0.0 0.0 chrM 16569 44951483 2712.9870843140807 2544.2104070414616 chrX 156040895 122958771 0.7879906802636578 3.5245242052875407 chrY 57227415 7936616 0.13868555831151905 0.9356419366200371 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 1442 0.006876195108459818 0.08260877747054356 GL000009.2 201709 860 0.004263567813037594 0.04163699725074754 GL000194.1 191469 334435 1.746679619155059 1.7720674639639304 GL000195.1 182896 50166 0.2742870265068673 0.33881116346526935 GL000205.2 185591 48820 0.26305154883588105 0.29421915912665914 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 15458 0.09592483881176814 0.23899421402238072 GL000219.1 179198 118409 0.6607718836147725 0.6909621751617468 GL000220.1 161802 0 0.0 0.0 GL000221.1 155397 0 0.0 0.0 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 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 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 1613 0.009214246950958271 0.08288326637038192 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 1581 0.03745557924662402 0.18987537710278257 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 5685 0.05667091989313768 0.4737523091414073 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 27594 0.014734410567510289 0.04757099255130037 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 0 0.0 0.0 KI270734.1 165050 222061 1.3454165404422902 3.2050751796443477 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 17500 0.11115910361298846 0.12355519220135838 KI270742.1 186739 56471 0.3024060319483343 0.33016237583622665 KI270743.1 210658 0 0.0 0.0 KI270744.1 168472 872 0.005175934279880336 0.08535805519103722 KI270745.1 41891 653 0.01558807381060371 0.12387528310958114 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 2855 0.01893964522163697 0.07020418191716052 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 110723048 479.2811327206853 524.114416270837