BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Cshl-CapTrap_HpreCap_0+_Brain01Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Cshl-CapTrap_HpreCap_0+_Brain01Rep1/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 8,204,419 number of mapped reads = 8,204,419 (100%) number of secondary alignments = 0 number of mapped bases = 75,478,282,494 bp number of sequenced bases = 5,456,761,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,601,927 duplication rate = 36.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 2.3237 >>>>>>> ACTG content number of A's = 1,357,282,507 bp (24.87%) number of C's = 1,351,343,481 bp (24.76%) number of T's = 1,379,727,139 bp (25.28%) number of G's = 1,368,408,569 bp (25.08%) number of N's = 0 bp (0%) GC percentage = 49.84% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 183,987,299 number of insertions = 35,427,308 mapped reads with insertion percentage = 89.69% number of deletions = 61,700,788 mapped reads with deletion percentage = 96.21% homopolymer indels = 34.32% >>>>>>> Coverage mean coverageData = 24.2646X std coverageData = 177.7908X There is a 2.24% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.68% of reference with a coverageData >= 5X There is a 0.61% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.48% of reference with a coverageData >= 9X There is a 0.45% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.37% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.33% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 7451584049 29.9312786918186 135.60496170690357 chr10 133797422 2214233273 16.549147508985637 82.55081051720305 chr11 135086622 3366213299 24.918924236627962 189.0252680464265 chr12 133275309 4073940234 30.567854350275788 186.65030596555795 chr13 114364328 1103800636 9.65161650755295 73.20662057149488 chr14 107043718 3025115094 28.26055699971109 208.3885506821752 chr15 101991189 2071531031 20.310882256701607 189.50933357450205 chr16 90338345 2325869772 25.74620746040898 304.45343615703933 chr17 83257441 3050536901 36.639810980978865 220.4949780345252 chr18 80373285 1761698149 21.918951664100828 127.18762789883358 chr19 58617616 4817699636 82.1885972981228 364.44283282733625 chr2 242193529 6822583849 28.16996753451658 298.5029260427673 chr20 64444167 2143841378 33.266647360031826 147.34073609138318 chr21 46709983 1713513227 36.68409014407049 196.54631146814768 chr22 50818468 1431309522 28.16514504136567 158.6427035496317 chr3 198295559 5332254849 26.890440087969896 140.67362107831724 chr4 190214555 3097786316 16.285748038576752 146.6298121612186 chr5 181538259 4633095794 25.52131886425109 145.37761154987672 chr6 170805979 3153851711 18.46452758541901 146.7911679874676 chr7 159345973 4026341954 25.26792411628752 184.50298553295124 chr8 145138636 3569445592 24.593352193278157 108.96238114271729 chr9 138394717 2056517387 14.859796902507485 141.1370990075842 chrIS 10567884 0 0.0 0.0 chrM 16569 12706780 766.9008389160481 723.019469179105 chrX 156040895 2068030563 13.253131898532112 104.7309599716111 chrY 57227415 132193056 2.3099602873902305 10.16929666346469 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 116550 0.55577013862066 0.5554188025015724 GL000009.2 201709 16657 0.08257935937414791 0.09311811196007487 GL000194.1 191469 5478770 28.61439710867033 28.50631749863102 GL000195.1 182896 1262754 6.904218791006911 6.8259842244823234 GL000205.2 185591 234493 1.2634933806057407 1.8231175597755516 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 2278 0.01654104764809248 0.04835059345389937 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 1516661 9.411661402322103 9.395162488485758 GL000219.1 179198 3035870 16.941427917722297 19.339499398714196 GL000220.1 161802 93454 0.5775824773488585 2.4364071911939824 GL000221.1 155397 97638 0.6283132879013108 0.6326474987498826 GL000224.1 179693 217696 1.211488483135125 2.114903980902932 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 31766 0.08102310609828572 0.09048180994366531 KI270448.1 7992 0 0.0 0.0 KI270465.1 1774 0 0.0 0.0 KI270466.1 1233 1090 0.884022708840227 0.7695033740466146 KI270467.1 3920 5271 1.3446428571428573 1.1520135038157153 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 0 0.0 0.0 KI270707.1 32032 0 0.0 0.0 KI270708.1 127682 0 0.0 0.0 KI270709.1 66860 309 0.004621597367633862 0.06782505588206575 KI270710.1 40176 0 0.0 0.0 KI270711.1 42210 1961 0.04645818526415541 0.20868080882803303 KI270712.1 176043 42741 0.2427872735638452 0.5106808592185493 KI270713.1 40745 20663 0.5071297091667689 1.3027005680311796 KI270714.1 41717 5790 0.13879233885466358 0.1626874475816391 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 12827 0.32017872297938194 0.3343199897489384 KI270718.1 38054 11315 0.29734062122247334 0.3358831796342753 KI270719.1 176845 1072 0.006061805535921287 0.07642459209332624 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 75495 0.7525718728816938 0.8346540788204697 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 61721 0.1376938658956649 0.18020751330638987 KI270728.1 1872759 127847 0.06826665897747655 0.08630141635175995 KI270729.1 280839 0 0.0 0.0 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 1497 0.009930084773870014 0.12994612031445665 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 411049 2.2865017911576886 5.045093208890594 KI270734.1 165050 3080826 18.666016358679187 48.98146580147444 KI270735.1 42811 0 0.0 0.0 KI270736.1 181920 106105 0.5832508795074758 0.5828019106732112 KI270737.1 103838 0 0.0 0.0 KI270738.1 99375 553 0.0055647798742138365 0.07405443006063549 KI270739.1 73985 0 0.0 0.0 KI270740.1 37240 0 0.0 0.0 KI270741.1 157432 230168 1.4620153463082475 1.5049816020195865 KI270742.1 186739 2895715 15.506750062922046 15.446836255121658 KI270743.1 210658 3317273 15.747196878352591 15.714343232934723 KI270744.1 168472 29920 0.17759627712616932 0.1899566933151699 KI270745.1 41891 0 0.0 0.0 KI270746.1 66486 0 0.0 0.0 KI270747.1 198735 38017 0.19129494049865398 0.19620156714818185 KI270748.1 93321 969 0.01038351496447745 0.1427661095441227 KI270749.1 158759 0 0.0 0.0 KI270750.1 148850 0 0.0 0.0 KI270751.1 150742 3661 0.02428652930172082 0.1056195785544805 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