BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/pacBioSII-Cshl-CapTrap_HpreCap_0+_Brain03Rep1.bam outfile = output/mappings/longReadMapping/bamqc/pacBioSII-Cshl-CapTrap_HpreCap_0+_Brain03Rep1/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 1,683,773 number of mapped reads = 1,683,773 (100%) number of secondary alignments = 0 number of mapped bases = 18,613,040,376 bp number of sequenced bases = 1,400,976,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,498,236 duplication rate = 36.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.1285 >>>>>>> ACTG content number of A's = 367,712,498 bp (26.25%) number of C's = 347,928,380 bp (24.83%) number of T's = 318,654,421 bp (22.75%) number of G's = 366,681,371 bp (26.17%) number of N's = 0 bp (0%) GC percentage = 51.01% >>>>>>> Mismatches and indels general error rate = 0.0002 number of mismatches = 2,602,049 number of insertions = 857,633 mapped reads with insertion percentage = 19.85% number of deletions = 353,554 mapped reads with deletion percentage = 12.63% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 5.9837X std coverageData = 36.9443X There is a 1.25% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.14% of reference with a coverageData >= 25X There is a 0.13% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.11% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 1791540608 7.196201622788426 27.744435325024845 chr10 133797422 570769052 4.265919652771785 16.795815447950382 chr11 135086622 938068070 6.944196665159041 42.24478733292264 chr12 133275309 1102616746 8.273225958155535 56.363686202721 chr13 114364328 214703334 1.8773627909569843 9.862493757083534 chr14 107043718 684055092 6.3904272458099785 54.873255820959265 chr15 101991189 582745382 5.713683581039534 31.40334575846209 chr16 90338345 709986493 7.859193048090487 64.5350868196759 chr17 83257441 667839151 8.021374942330981 44.42303997224171 chr18 80373285 635101903 7.901903014166958 57.871453277874174 chr19 58617616 1233218562 21.038360925493798 80.2158974458965 chr2 242193529 1491133573 6.1567853573825255 30.06079708724566 chr20 64444167 641949778 9.961332543874763 26.359580097851545 chr21 46709983 303716626 6.502178046179122 37.29998758636288 chr22 50818468 398019095 7.832174220600275 42.24217839777725 chr3 198295559 1345457157 6.785109882365041 25.13490836129104 chr4 190214555 592011172 3.112333711791929 14.507049684701723 chr5 181538259 954409891 5.25734848542312 21.573656468489645 chr6 170805979 705098837 4.128068824803844 27.335603195310124 chr7 159345973 915615198 5.746083071707122 36.09495336865161 chr8 145138636 788407361 5.4320984592965305 24.408147817857863 chr9 138394717 523252559 3.780870905643024 36.68682267046879 chrIS 10567884 0 0.0 0.0 chrM 16569 4194638 253.16180819602872 231.160299536588 chrX 156040895 629687925 4.035403187093999 29.662369119275834 chrY 57227415 20947910 0.36604676272726977 1.7873722785004993 ERCC-00002 1061 12864038 12124.446748350612 1054.8921722552248 ERCC-00003 1023 17147 16.761485826001955 1.5907237122332973 ERCC-00004 523 66523 127.19502868068834 14.838168953486612 ERCC-00009 984 359592 365.4390243902439 30.883819892495502 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 9330 14.487577639751553 1.7853793906868842 ERCC-00022 751 37218 49.55792276964048 4.737858606105378 ERCC-00024 536 0 0.0 0.0 ERCC-00025 1994 834 0.4182547642928786 0.4932724565989745 ERCC-00028 1130 0 0.0 0.0 ERCC-00031 1138 1130 0.9929701230228472 0.09334461669518027 ERCC-00033 2022 0 0.0 0.0 ERCC-00034 1019 5065 4.970559371933268 0.3361106136533038 ERCC-00035 1130 21322 18.869026548672565 1.4828621312323094 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 6899 6.743890518084067 0.6444736997698499 ERCC-00043 1023 19782 19.33724340175953 1.1310502335032386 ERCC-00044 1156 19581 16.938581314878892 0.8115039869284484 ERCC-00046 522 262138 502.1800766283525 58.743674048894455 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 266 0.9708029197080292 0.16835857802439108 ERCC-00053 1023 2029 1.9833822091886608 0.1788348778753166 ERCC-00054 274 538 1.9635036496350364 0.18752164348416372 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 0 0.0 0.0 ERCC-00059 525 6203 11.815238095238096 1.4349900250113397 ERCC-00060 523 4771 9.122370936902486 1.290806588151529 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 12190 11.915933528836755 0.9291972405683098 ERCC-00067 644 0 0.0 0.0 ERCC-00069 1137 0 0.0 0.0 ERCC-00071 642 24112 37.557632398753896 3.8444437656641344 ERCC-00073 603 0 0.0 0.0 ERCC-00074 522 486817 932.5996168582376 111.02476154861947 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 73761 114.89252336448598 12.265431800287296 ERCC-00077 273 0 0.0 0.0 ERCC-00078 993 13396 13.49043303121853 1.1975802700945821 ERCC-00079 644 27350 42.46894409937888 4.513762288609217 ERCC-00081 534 0 0.0 0.0 ERCC-00083 1022 0 0.0 0.0 ERCC-00084 994 4243 4.268611670020121 0.44323745413617804 ERCC-00085 844 844 1.0 0.0 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 126640 112.66903914590748 8.83181679097993 ERCC-00095 521 1544 2.963531669865643 0.32285643823097565 ERCC-00096 1107 10857939 9808.436314363144 817.4889334480745 ERCC-00097 523 0 0.0 0.0 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 2682 1.9866666666666666 0.1604007327343859 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 229312 224.3757338551859 18.91139776165697 ERCC-00109 536 531 0.9906716417910447 0.0961318882685693 ERCC-00111 994 168538 169.5553319919517 14.39058230616107 ERCC-00112 1136 37056 32.61971830985915 2.5165145867931202 ERCC-00113 840 1388190 1652.607142857143 142.19118794275343 ERCC-00116 1991 27037 13.5796082370668 0.8215848072949619 ERCC-00117 1136 0 0.0 0.0 ERCC-00120 536 528 0.9850746268656716 0.12125430454680428 ERCC-00123 1022 0 0.0 0.0 ERCC-00126 1118 6679 5.974060822898032 0.3830489798609013 ERCC-00130 1059 4934908 4659.969782813975 334.2098418612459 ERCC-00131 771 43172 55.99481193255512 5.4368053828441045 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 401675 388.8431752178122 27.550435553643933 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 1548 1.9744897959183674 0.2186746835891511 ERCC-00144 538 9533 17.719330855018587 2.0804538033999793 ERCC-00145 1042 117286 112.55854126679462 9.897353572071369 ERCC-00147 1023 0 0.0 0.0 ERCC-00148 494 3405 6.892712550607287 0.8189478848013534 ERCC-00150 743 0 0.0 0.0 ERCC-00154 537 528 0.9832402234636871 0.12837011500643677 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 5145 6.924629878869448 0.6997204529453968 ERCC-00162 523 513 0.9808795411089866 0.13694840978562095 ERCC-00163 543 4816 8.869244935543279 1.0370057655146194 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 32828 37.64678899082569 3.532017751682259 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 1015 0.9921798631476051 0.09338742304752021 ERCC-00171 505 1010567 2001.1227722772278 241.55819005049727 GL000008.2 209709 0 0.0 0.0 GL000009.2 201709 0 0.0 0.0 GL000194.1 191469 1719115 8.978555275266492 8.950813992481658 GL000195.1 182896 122843 0.6716549295774648 0.7044544648789738 GL000205.2 185591 29057 0.156564704107419 0.3015982607097932 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 605395 3.7567872811780547 3.7481311895534657 GL000219.1 179198 744321 4.153623366332214 4.8402545419094185 GL000220.1 161802 47934 0.29625097341194795 0.6142418725896176 GL000221.1 155397 0 0.0 0.0 GL000224.1 179693 32045 0.1783319327964918 0.382809247698793 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 0 0.0 0.0 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 431 0.010210850509357971 0.10053153257179319 KI270712.1 176043 1053 0.0059814931579216446 0.12256852204326284 KI270713.1 40745 7769 0.1906737022947601 0.49410326679084543 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 6298 0.06278161011204593 0.1358350558863811 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 88 1.9631989434420232E-4 0.014010044712394283 KI270728.1 1872759 0 0.0 0.0 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 37121 0.20648933093028948 0.7828039493811284 KI270734.1 165050 2134227 12.930790669494092 32.25290990962807 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 13750 0.08733929569591951 0.14734760255477505 KI270742.1 186739 528599 2.830683467299279 2.8211839967824943 KI270743.1 210658 138200 0.656039647200676 0.6555008520578025 KI270744.1 168472 0 0.0 0.0 KI270745.1 41891 0 0.0 0.0 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 128565283 556.5138927966964 631.6651362879924