BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain03Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-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 = 13,689,397 number of mapped reads = 13,689,397 (100%) number of secondary alignments = 0 number of mapped bases = 132,612,739,247 bp number of sequenced bases = 9,773,652,545 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,812,543 duplication rate = 38.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.4429 >>>>>>> ACTG content number of A's = 2,366,790,066 bp (24.22%) number of C's = 2,487,738,229 bp (25.45%) number of T's = 2,419,609,986 bp (24.76%) number of G's = 2,499,514,264 bp (25.57%) number of N's = 0 bp (0%) GC percentage = 51.03% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 359,893,611 number of insertions = 73,162,488 mapped reads with insertion percentage = 94.27% number of deletions = 118,448,553 mapped reads with deletion percentage = 97.94% homopolymer indels = 34.05% >>>>>>> Coverage mean coverageData = 42.6321X std coverageData = 290.5596X There is a 2.78% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 1.22% of reference with a coverageData >= 3X There is a 1.01% of reference with a coverageData >= 4X There is a 0.89% of reference with a coverageData >= 5X There is a 0.8% of reference with a coverageData >= 6X There is a 0.73% of reference with a coverageData >= 7X There is a 0.68% of reference with a coverageData >= 8X There is a 0.64% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.57% of reference with a coverageData >= 11X There is a 0.54% of reference with a coverageData >= 12X There is a 0.52% of reference with a coverageData >= 13X There is a 0.5% of reference with a coverageData >= 14X There is a 0.48% of reference with a coverageData >= 15X There is a 0.46% of reference with a coverageData >= 16X There is a 0.45% of reference with a coverageData >= 17X There is a 0.43% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.41% of reference with a coverageData >= 20X There is a 0.4% of reference with a coverageData >= 21X There is a 0.39% of reference with a coverageData >= 22X There is a 0.38% of reference with a coverageData >= 23X There is a 0.37% of reference with a coverageData >= 24X There is a 0.36% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.32% of reference with a coverageData >= 31X There is a 0.31% of reference with a coverageData >= 32X There is a 0.31% of reference with a coverageData >= 33X There is a 0.3% of reference with a coverageData >= 34X There is a 0.3% of reference with a coverageData >= 35X There is a 0.29% of reference with a coverageData >= 36X There is a 0.29% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.28% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.27% of reference with a coverageData >= 41X There is a 0.27% of reference with a coverageData >= 42X There is a 0.26% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.25% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.25% of reference with a coverageData >= 48X There is a 0.24% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 12758481893 51.247852095978466 224.88431574288612 chr10 133797422 4016740047 30.021057109755073 139.28445390369532 chr11 135086622 6293851574 46.591227767913246 323.2722768709007 chr12 133275309 8209686486 61.59945565010845 313.99464210880467 chr13 114364328 1752004634 15.319502721163193 92.8341024957677 chr14 107043718 5554744251 51.89229554788073 520.3201011522737 chr15 101991189 3791568469 37.175451195102745 250.9290943879938 chr16 90338345 4836418660 53.53671976169145 512.5154965272922 chr17 83257441 5250750845 63.06644525622641 346.50498591321224 chr18 80373285 2828819779 35.196020406531844 194.33556355969037 chr19 58617616 9355904204 159.60908754801628 649.0185878737111 chr2 242193529 10727462434 44.2929358116748 331.50839523946365 chr20 64444167 3560804317 55.25409796979764 181.48861003056865 chr21 46709983 2783209852 59.58490398080428 346.09832651110054 chr22 50818468 2606025901 51.28107956737303 268.3908780803011 chr3 198295559 9230443463 46.54891672586576 218.85607253394255 chr4 190214555 4508698306 23.703224529794788 165.71820522958097 chr5 181538259 7473638819 41.168395357366514 198.8717660447856 chr6 170805979 5405966508 31.649749848627955 221.43128151179417 chr7 159345973 6737146471 42.27999204598663 292.2839691785424 chr8 145138636 5451344065 37.559565221489336 137.49741531863603 chr9 138394717 3997493319 28.8847248338244 286.50463679670037 chrIS 10567884 0 0.0 0.0 chrM 16569 29929191 1806.3365924316495 1562.4134719028923 chrX 156040895 3905816658 25.030724528976844 201.65836001300048 chrY 57227415 198902691 3.4756539501216333 14.715857982722065 ERCC-00002 1061 107360386 101187.92271442036 10637.384168227514 ERCC-00003 1023 135051 132.01466275659823 14.497720685697828 ERCC-00004 523 761639 1456.2887189292544 209.28036806494657 ERCC-00009 984 3057674 3107.392276422764 317.08976201510933 ERCC-00012 994 0 0.0 0.0 ERCC-00013 808 2389 2.9566831683168315 0.39150208487631805 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 88929 138.0885093167702 16.800015669743033 ERCC-00022 751 442109 588.693741677763 66.31958340571701 ERCC-00024 536 0 0.0 0.0 ERCC-00025 1994 15615 7.83099297893681 1.0185615931818532 ERCC-00028 1130 3352 2.966371681415929 0.37029873452648676 ERCC-00031 1138 3373 2.9639718804920916 0.33321195113494206 ERCC-00033 2022 0 0.0 0.0 ERCC-00034 1019 53841 52.837095191364085 5.704610845677978 ERCC-00035 1130 179510 158.858407079646 13.860048332383858 ERCC-00039 740 8761 11.83918918918919 1.1170232996060028 ERCC-00040 744 2186 2.9381720430107525 0.4487556825489289 ERCC-00041 1122 0 0.0 0.0 ERCC-00042 1023 60901 59.531769305962854 5.808091602345714 ERCC-00043 1023 257890 252.09188660801564 21.109294604809048 ERCC-00044 1156 152952 132.3114186851211 10.128149296529704 ERCC-00046 522 3099053 5936.883141762452 805.0749680933561 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 781 2.8503649635036497 0.613627281862865 ERCC-00053 1023 9114 8.909090909090908 0.867832067856747 ERCC-00054 274 5760 21.021897810218977 3.920577864311923 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 3379 2.9744718309859155 0.3264516072933102 ERCC-00059 525 74016 140.98285714285714 18.422760545652483 ERCC-00060 523 79876 152.7265774378585 22.412429204411815 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 87103 85.1446725317693 8.069002336413917 ERCC-00067 644 12583 19.538819875776397 2.5528087265957717 ERCC-00069 1137 3326 2.925241864555849 0.3835479565158259 ERCC-00071 642 261443 407.23208722741435 45.87001049585143 ERCC-00073 603 2354 3.9038142620232175 0.6158334097967086 ERCC-00074 522 6559213 12565.54214559387 1645.9648304006364 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 763726 1189.6043613707166 140.25605143622153 ERCC-00077 273 0 0.0 0.0 ERCC-00078 993 113997 114.80060422960725 11.366724909713435 ERCC-00079 644 236022 366.49378881987576 44.56586761271698 ERCC-00081 534 509 0.9531835205992509 0.24474587977375994 ERCC-00083 1022 0 0.0 0.0 ERCC-00084 994 31414 31.603621730382294 4.906558789453443 ERCC-00085 844 9986 11.83175355450237 1.3120709923922127 ERCC-00086 1020 1014 0.9941176470588236 0.13580466330135546 ERCC-00092 1124 923063 821.2304270462633 82.23453457125122 ERCC-00095 521 21703 41.65642994241843 5.512374423649232 ERCC-00096 1107 79852501 72134.14724480578 6892.137213507476 ERCC-00097 523 1535 2.9349904397705546 0.47738390927196145 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 23266 17.234074074074073 1.8168925370212778 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 2071843 2027.2436399217222 208.0484425570805 ERCC-00109 536 525 0.9794776119402985 0.1806236103520753 ERCC-00111 994 1630517 1640.3591549295775 155.4657095244133 ERCC-00112 1136 287612 253.17957746478874 23.34183692262515 ERCC-00113 840 15057938 17926.116666666665 1785.25861813102 ERCC-00116 1991 98321 49.38272225012557 4.334041458499195 ERCC-00117 1136 0 0.0 0.0 ERCC-00120 536 5183 9.669776119402986 1.6328016705615926 ERCC-00123 1022 0 0.0 0.0 ERCC-00126 1118 18850 16.86046511627907 1.3139020364488874 ERCC-00130 1059 40496139 38239.98016997167 3734.9368897619324 ERCC-00131 771 342459 444.1750972762646 49.50958614092193 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 3359981 3252.6437560503387 284.1094919548329 ERCC-00137 537 2081 3.8752327746741155 0.6801457698104892 ERCC-00138 1024 1008 0.984375 0.17737988343348013 ERCC-00142 493 1468 2.977687626774848 0.31574013316057825 ERCC-00143 784 8926 11.385204081632653 1.4593375293512745 ERCC-00144 538 105732 196.5278810408922 27.745242646584177 ERCC-00145 1042 1010205 969.4865642994242 104.52920846606074 ERCC-00147 1023 1016 0.9931573802541545 0.14245614066303208 ERCC-00148 494 23701 47.977732793522264 7.027441277722113 ERCC-00150 743 11710 15.76043068640646 1.6527947045933382 ERCC-00154 537 17518 32.621973929236496 4.17229720580756 ERCC-00156 494 1460 2.9554655870445345 0.3836339491835785 ERCC-00157 1019 19711 19.343473994111875 2.0275798049121656 ERCC-00158 1027 2041 1.9873417721518987 0.18007841380940628 ERCC-00160 743 66686 89.75235531628533 10.126943703712818 ERCC-00162 523 6544 12.51242829827916 2.0457747327801363 ERCC-00163 543 52074 95.90055248618785 11.996731356533893 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 292600 335.55045871559633 35.12576647081802 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 68227 66.6930596285435 7.150687968678603 ERCC-00171 505 10756952 21300.89504950495 3127.143083944838 GL000008.2 209709 0 0.0 0.0 GL000009.2 201709 0 0.0 0.0 GL000194.1 191469 10025088 52.35880481957915 52.264690684122336 GL000195.1 182896 675304 3.6922841396203308 3.757834297698164 GL000205.2 185591 275753 1.4858101955374992 2.362362001940084 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 11423 0.0829448583336964 0.18459180334562544 GL000216.2 176608 0 0.0 0.0 GL000218.1 161147 2549775 15.822665020136894 15.755423158034429 GL000219.1 179198 4313847 24.073075592361523 30.197839045637192 GL000220.1 161802 283275 1.750750917788408 3.270961905227315 GL000221.1 155397 26704 0.17184372928692318 0.22585569781397427 GL000224.1 179693 264207 1.4703243865926887 2.8079646779728544 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 9297 0.08263632727434336 0.11119211466624102 KI270442.1 392061 63644 0.16233188202856189 0.18628395146002882 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 889 0.005078403930193368 0.07088258880182964 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 7830 0.18550106609808104 0.3552197282366157 KI270712.1 176043 77970 0.442903154342973 0.6804742913307399 KI270713.1 40745 34690 0.8513928089336115 3.6520665176688754 KI270714.1 41717 5780 0.13855262842486277 0.16872344311338955 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 445 0.011107782936448506 0.10445659267683545 KI270718.1 38054 3456 0.09081831082146423 0.16956097858877114 KI270719.1 176845 249 0.0014080126664593288 0.03704318686187619 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 58593 0.5840842936321224 0.7551648535059419 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 21751 0.12586655864822638 0.13107387168991155 KI270726.1 43739 0 0.0 0.0 KI270727.1 448248 54753 0.12214889971622851 0.18190003848170716 KI270728.1 1872759 147983 0.07901870982865387 0.22404640482334057 KI270729.1 280839 0 0.0 0.0 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 1601 0.010619950382742747 0.14424295315863386 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 592475 3.2957023340675966 7.388080552742929 KI270734.1 165050 13116033 79.46702817328082 193.81369031210048 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 113051 0.7180941612886834 1.0744875588487122 KI270742.1 186739 4276521 22.901059767911363 22.837437176632136 KI270743.1 210658 3040243 14.432126954589904 14.396181303655219 KI270744.1 168472 6954 0.0412768887411558 0.06685949351957465 KI270745.1 41891 413 0.009858919576997445 0.11938728707928749 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 8323 0.05521354367064255 0.0884125626714629 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 1026235767 4442.213701037577 5067.970019822383