BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Heart02Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-CapTrap_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 = 15,302,379 number of mapped reads = 15,302,379 (100%) number of secondary alignments = 0 number of mapped bases = 148,253,330,652 bp number of sequenced bases = 11,185,794,883 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,687,573 duplication rate = 39.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.8091 >>>>>>> ACTG content number of A's = 2,701,671,862 bp (24.15%) number of C's = 2,842,950,269 bp (25.42%) number of T's = 2,816,087,895 bp (25.18%) number of G's = 2,825,084,857 bp (25.26%) number of N's = 0 bp (0%) GC percentage = 50.67% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 344,673,283 number of insertions = 69,820,104 mapped reads with insertion percentage = 91.48% number of deletions = 113,336,823 mapped reads with deletion percentage = 96.64% homopolymer indels = 35.02% >>>>>>> Coverage mean coverageData = 47.6602X std coverageData = 987.5917X There is a 1.92% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.92% of reference with a coverageData >= 3X There is a 0.79% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.64% of reference with a coverageData >= 6X There is a 0.59% of reference with a coverageData >= 7X There is a 0.55% of reference with a coverageData >= 8X There is a 0.52% of reference with a coverageData >= 9X There is a 0.49% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.45% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.42% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.39% of reference with a coverageData >= 16X There is a 0.38% 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 0.32% of reference with a coverageData >= 24X There is a 0.31% of reference with a coverageData >= 25X There is a 0.31% of reference with a coverageData >= 26X There is a 0.3% of reference with a coverageData >= 27X There is a 0.29% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.27% of reference with a coverageData >= 33X There is a 0.27% of reference with a coverageData >= 34X There is a 0.26% of reference with a coverageData >= 35X There is a 0.26% of reference with a coverageData >= 36X There is a 0.26% of reference with a coverageData >= 37X There is a 0.25% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.24% 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 0.23% 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 0.22% 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 13870733654 55.71550853185061 321.0672789762575 chr10 133797422 4609986457 34.45497221164695 134.68701537114956 chr11 135086622 7984497464 59.10650030171011 623.414411254212 chr12 133275309 23406122286 175.62234491611645 4360.93811051083 chr13 114364328 2119883828 18.536232976422507 345.88919588744125 chr14 107043718 3751972553 35.05084299295359 177.04463614014838 chr15 101991189 6091930788 59.72997126251759 513.6043366067319 chr16 90338345 3319757968 36.74804943570751 299.1318720846546 chr17 83257441 4322501034 51.91729390289572 1380.2570807462052 chr18 80373285 1987630053 24.72998401147844 423.92116436860636 chr19 58617616 8075076976 137.7585362052254 783.3446117067192 chr2 242193529 9309095860 38.43660026110772 291.3225864444807 chr20 64444167 2235099176 34.68272273579081 170.2009261049193 chr21 46709983 2292856495 49.08707620381707 313.97256235657113 chr22 50818468 3951471020 77.75659470883696 832.5930623863205 chr3 198295559 7415593948 37.39667184377034 426.7222998768787 chr4 190214555 6904952894 36.30086506261311 155.29150310467702 chr5 181538259 7942528227 43.751263622066574 254.25390477716212 chr6 170805979 6963263190 40.76709276084533 223.4518371339271 chr7 159345973 6616861102 41.52512283445029 279.5458439934663 chr8 145138636 6305387717 43.443895373248516 194.57451677620676 chr9 138394717 3625021348 26.193350632018706 265.0813296935842 chrIS 10567884 0 0.0 0.0 chrM 16569 37273087 2249.5676866437325 1969.7047634303367 chrX 156040895 4211640617 26.990620740800033 222.951065839244 chrY 57227415 432575129 7.558879411205276 51.76305063767712 ERCC-00002 1061 26253178 24743.805843543825 2630.1988743563375 ERCC-00003 1023 119380 116.69599217986315 16.919164647211346 ERCC-00004 523 1268427 2425.2906309751434 349.97559488904415 ERCC-00009 984 707487 718.9908536585366 73.52900479928144 ERCC-00012 994 0 0.0 0.0 ERCC-00013 808 795 0.9839108910891089 0.143601693676714 ERCC-00014 1957 387 0.19775166070516095 0.39597045927322516 ERCC-00016 844 0 0.0 0.0 ERCC-00017 1136 0 0.0 0.0 ERCC-00019 644 22550 35.015527950310556 4.340362938051495 ERCC-00022 751 135337 180.20905459387484 20.453526315697083 ERCC-00024 536 0 0.0 0.0 ERCC-00025 1994 9906 4.9679037111334 0.8305229692786189 ERCC-00028 1130 2237 1.979646017699115 0.27397778460067784 ERCC-00031 1138 1102 0.968365553602812 0.23521872770797925 ERCC-00033 2022 0 0.0 0.0 ERCC-00034 1019 14424 14.155053974484789 1.6164263274761266 ERCC-00035 1130 43349 38.361946902654864 3.5588353363659064 ERCC-00039 740 3668 4.956756756756757 0.3920223454819771 ERCC-00040 744 2201 2.9583333333333335 0.375 ERCC-00041 1122 0 0.0 0.0 ERCC-00042 1023 55790 54.535679374389055 8.09720564439057 ERCC-00043 1023 72473 70.8435972629521 5.491122625831778 ERCC-00044 1156 34446 29.79757785467128 2.2398764722707174 ERCC-00046 522 3442386 6594.609195402299 906.2822527597759 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 266 0.9708029197080292 0.16835857802439108 ERCC-00053 1023 12933 12.642228739002933 1.5173650780920986 ERCC-00054 274 3923 14.317518248175183 2.9072384269140166 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 1349 1.1875 0.4839524224374733 ERCC-00059 525 17301 32.95428571428572 4.534325621692555 ERCC-00060 523 53628 102.53919694072658 14.728225250188382 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 47152 46.09188660801564 4.75425622315805 ERCC-00067 644 2711 4.209627329192546 0.819259426240724 ERCC-00069 1137 1129 0.9929639401934917 0.09791806009693957 ERCC-00071 642 62173 96.84267912772586 10.486493218328663 ERCC-00073 603 0 0.0 0.0 ERCC-00074 522 8020567 15365.070881226053 2034.4293130422152 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 203926 317.6417445482866 37.41442800768503 ERCC-00077 273 263 0.9633699633699634 0.24300378447797782 ERCC-00078 993 18839 18.971802618328297 1.9737357917520797 ERCC-00079 644 67648 105.04347826086956 13.512494093406982 ERCC-00081 534 0 0.0 0.0 ERCC-00083 1022 0 0.0 0.0 ERCC-00084 994 2245 2.2585513078470827 0.46384379630433287 ERCC-00085 844 0 0.0 0.0 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 221921 197.43861209964413 20.0750990545596 ERCC-00095 521 37713 72.38579654510556 9.40873324404036 ERCC-00096 1107 18981668 17146.944896115627 1637.1000200958474 ERCC-00097 523 0 0.0 0.0 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 10681 7.911851851851852 0.8384311562918455 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 468939 458.8444227005871 47.4326192381081 ERCC-00109 536 0 0.0 0.0 ERCC-00111 994 395957 398.3470824949698 39.089982875036334 ERCC-00112 1136 62120 54.683098591549296 4.965313127834874 ERCC-00113 840 3297642 3925.7642857142855 395.8976595494529 ERCC-00116 1991 17408 8.743345052737318 1.121481618365782 ERCC-00117 1136 0 0.0 0.0 ERCC-00120 536 2093 3.904850746268657 0.6265852028932224 ERCC-00123 1022 0 0.0 0.0 ERCC-00126 1118 4298 3.8443649373881934 0.471276462144491 ERCC-00130 1059 9870602 9320.681775259678 905.3401635399829 ERCC-00131 771 91219 118.31258106355382 13.437658735012528 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 909037 879.9970958373669 78.30109987880813 ERCC-00137 537 0 0.0 0.0 ERCC-00138 1024 0 0.0 0.0 ERCC-00142 493 484 0.9817444219066938 0.13387423935091247 ERCC-00143 784 3850 4.910714285714286 0.6721297359321335 ERCC-00144 538 28891 53.70074349442379 7.299548066193892 ERCC-00145 1042 241034 231.3186180422265 24.707784392447525 ERCC-00147 1023 0 0.0 0.0 ERCC-00148 494 7712 15.611336032388664 2.1655888989042276 ERCC-00150 743 2936 3.9515477792732168 0.46460093354454596 ERCC-00154 537 1364 2.5400372439478587 0.647399559016509 ERCC-00156 494 0 0.0 0.0 ERCC-00157 1019 6492 6.370951913640824 0.8903457954673207 ERCC-00158 1027 0 0.0 0.0 ERCC-00160 743 12398 16.686406460296098 2.0153931950510104 ERCC-00162 523 10051 19.217973231357554 2.6287613245892874 ERCC-00163 543 17936 33.03130755064457 4.253544479582328 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 63281 72.56995412844037 8.14841530266478 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 15092 14.75268817204301 1.586009079262762 ERCC-00171 505 3433540 6799.089108910891 1005.4152307269997 GL000008.2 209709 428792 2.0447000367175465 2.028447746780012 GL000009.2 201709 84293 0.41789409495857893 0.46038941868085764 GL000194.1 191469 18604791 97.1686852702004 97.12450965462477 GL000195.1 182896 2847121 15.566885005686292 16.822470418130848 GL000205.2 185591 2481493 13.37076151321993 17.80920322188072 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 265686 1.9292031542717727 1.9043140078670484 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 10804592 67.04804929660496 67.2842347072654 GL000219.1 179198 846358 4.723032623131955 4.934547354915833 GL000220.1 161802 276217 1.7071297017342184 9.811717486422038 GL000221.1 155397 482104 3.102402234277367 3.0894250665801395 GL000224.1 179693 180347 1.0036395407723173 1.0877213678945417 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 825 0.002104264387429507 0.03494330866839777 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 208213 1.1894147553626002 1.1839549386040127 KI270707.1 32032 0 0.0 0.0 KI270708.1 127682 0 0.0 0.0 KI270709.1 66860 211 0.003155848040682022 0.05608822214891595 KI270710.1 40176 0 0.0 0.0 KI270711.1 42210 8305 0.19675432361999526 0.35387413680873864 KI270712.1 176043 1911 0.01085530239770965 0.10305709877234329 KI270713.1 40745 22159 0.5438458706589766 0.5747400235733459 KI270714.1 41717 16793 0.4025457247644845 0.5530649675376125 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 94 0.0024701739633152886 0.049639421873207266 KI270719.1 176845 140 7.916537080494218E-4 0.028024654791676738 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 138122 1.3768690936640218 5.602053335018092 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 27891 0.062222251967660756 0.1015109149433129 KI270728.1 1872759 1094603 0.5844868453442221 2.100479910536244 KI270729.1 280839 0 0.0 0.0 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 750 0.0049749923716783636 0.09788373414578017 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 307558 1.7108225975124045 8.907455813132428 KI270734.1 165050 6871931 41.63544986367767 104.76801751861177 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 247190 1.5701382184054067 1.6237564480852609 KI270742.1 186739 15674395 83.93744745339752 83.7427176575133 KI270743.1 210658 553143 2.625786820343875 2.6195091182865022 KI270744.1 168472 103604 0.6149627237760578 0.8447872434787455 KI270745.1 41891 1174 0.028025112792723975 0.16339798793448831 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 154838 1.0271722545806743 1.0232771527193776 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 327960202 1419.6243685584302 1534.3731806753426