BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep5.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep5/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 13,811,609 number of mapped reads = 13,811,609 (100%) number of secondary alignments = 0 number of mapped bases = 94,904,395,932 bp number of sequenced bases = 7,585,812,709 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,806,986 duplication rate = 37.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.5753 >>>>>>> ACTG content number of A's = 1,926,397,552 bp (25.39%) number of C's = 1,839,015,808 bp (24.24%) number of T's = 1,968,762,278 bp (25.95%) number of G's = 1,851,637,071 bp (24.41%) number of N's = 0 bp (0%) GC percentage = 48.65% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 238,567,308 number of insertions = 49,662,015 mapped reads with insertion percentage = 87.32% number of deletions = 78,325,343 mapped reads with deletion percentage = 93.48% homopolymer indels = 33.87% >>>>>>> Coverage mean coverageData = 30.5097X std coverageData = 279.8753X There is a 2.66% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.97% of reference with a coverageData >= 4X There is a 0.84% of reference with a coverageData >= 5X There is a 0.75% of reference with a coverageData >= 6X There is a 0.69% of reference with a coverageData >= 7X There is a 0.63% of reference with a coverageData >= 8X There is a 0.59% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.52% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.47% of reference with a coverageData >= 13X There is a 0.45% of reference with a coverageData >= 14X There is a 0.43% of reference with a coverageData >= 15X There is a 0.41% of reference with a coverageData >= 16X There is a 0.4% of reference with a coverageData >= 17X There is a 0.38% of reference with a coverageData >= 18X There is a 0.37% of reference with a coverageData >= 19X There is a 0.36% of reference with a coverageData >= 20X There is a 0.35% of reference with a coverageData >= 21X There is a 0.34% of reference with a coverageData >= 22X There is a 0.33% 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 0.3% 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 0.28% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 9106852747 36.580107770829066 183.47877689229782 chr10 133797422 2762495838 20.646854002911954 133.5174092528444 chr11 135086622 4288963449 31.749727585904104 301.7844083982703 chr12 133275309 4103521558 30.789810871869747 212.35903778407175 chr13 114364328 1448185265 12.662910632413283 122.41771017245833 chr14 107043718 4325755976 40.411114793303426 390.0244494261325 chr15 101991189 2449237861 24.014210296146267 287.38109541041825 chr16 90338345 2761402110 30.567331181460098 406.26561487544774 chr17 83257441 3900917018 46.85367423195243 350.62757975548675 chr18 80373285 2025942822 25.206669380254894 174.9814563320482 chr19 58617616 6122187765 104.44279694008709 491.4003111207471 chr2 242193529 8122980336 33.53921291596523 466.5010264046876 chr20 64444167 2025251084 31.426445220402957 301.7813574344917 chr21 46709983 3030258100 64.87388573872956 348.39578593473504 chr22 50818468 1596101571 31.40790413044329 203.828120283929 chr3 198295559 6355165471 32.048955120573325 232.33319095226238 chr4 190214555 3724272345 19.579323701070088 215.19912948323824 chr5 181538259 6243915382 34.39448751130747 239.98617034697892 chr6 170805979 4246812448 24.863371135269215 243.0535597565168 chr7 159345973 4931211651 30.94657215466625 285.4813737354467 chr8 145138636 4746358830 32.70224222032788 196.09665041139127 chr9 138394717 2616378204 18.90518844010498 219.26886561190625 chrIS 10567884 0 0.0 0.0 chrM 16569 102978756 6215.146116241173 6992.087709747693 chrX 156040895 2365456205 15.159206854075016 160.54466581767034 chrY 57227415 177424673 3.100344004704738 11.880992506942958 ERCC-00002 1061 37512484 35355.78133836004 4756.545308419098 ERCC-00003 1023 717103 700.980449657869 74.64042865921164 ERCC-00004 523 9732092 18608.206500956025 2573.875438446543 ERCC-00009 984 1224215 1244.1209349593496 150.42807424363056 ERCC-00012 994 0 0.0 0.0 ERCC-00013 808 0 0.0 0.0 ERCC-00014 1957 385 0.19672968829841594 0.39713622870506293 ERCC-00016 844 827 0.9798578199052133 0.18579241797799317 ERCC-00017 1136 0 0.0 0.0 ERCC-00019 644 54107 84.01708074534162 10.19618083417793 ERCC-00022 751 225381 300.10785619174436 34.91374800417347 ERCC-00024 536 524 0.9776119402985075 0.17033898821661714 ERCC-00025 1994 1795 0.9002006018054163 0.3172970348954517 ERCC-00028 1130 1121 0.9920353982300885 0.14776641255422301 ERCC-00031 1138 591 0.5193321616871704 0.4998300927335667 ERCC-00033 2022 2011 0.9945598417408507 0.09135445354232899 ERCC-00034 1019 24396 23.941118743866536 2.5315670647244306 ERCC-00035 1130 46815 41.42920353982301 3.7150106243761813 ERCC-00039 740 2915 3.939189189189189 0.5206737642097056 ERCC-00040 744 4393 5.904569892473118 0.7746682665684204 ERCC-00041 1122 0 0.0 0.0 ERCC-00042 1023 197818 193.3704789833822 18.972068028372693 ERCC-00043 1023 269105 263.05474095796677 22.603855442080896 ERCC-00044 1156 34872 30.166089965397923 4.020372995804596 ERCC-00046 522 17812480 34123.52490421456 4569.132313172701 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 32602 118.98540145985402 19.911222057238696 ERCC-00053 1023 40381 39.473118279569896 3.6470005192768626 ERCC-00054 274 14872 54.277372262773724 10.78900020580622 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 0 0.0 0.0 ERCC-00059 525 54305 103.43809523809524 13.21180809033627 ERCC-00060 523 1301031 2487.6309751434032 350.4326875046279 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 113941 111.37927663734115 10.846401369031998 ERCC-00067 644 7100 11.024844720496894 2.2100370414075265 ERCC-00069 1137 0 0.0 0.0 ERCC-00071 642 118681 184.8613707165109 20.80008608626008 ERCC-00073 603 1183 1.9618573797678276 0.31861950545877227 ERCC-00074 522 54679628 104750.24521072797 13666.275410319122 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 391245 609.4158878504672 70.97112241541569 ERCC-00077 273 1837 6.728937728937729 1.221511492887056 ERCC-00078 993 32422 32.65055387713998 8.319174909299242 ERCC-00079 644 166398 258.38198757763973 30.69135655070596 ERCC-00081 534 0 0.0 0.0 ERCC-00083 1022 0 0.0 0.0 ERCC-00084 994 4326 4.352112676056338 3.2551930690595348 ERCC-00085 844 5886 6.9739336492890995 0.3800271181092418 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 303468 269.98932384341634 39.614778064201694 ERCC-00095 521 275585 528.9539347408829 65.33911425709411 ERCC-00096 1107 26085726 23564.341463414636 2664.862800059738 ERCC-00097 523 2496 4.772466539196941 0.6803364506053794 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 21454 15.891851851851852 2.1394046836792495 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 731999 716.2416829745597 72.13196592836873 ERCC-00109 536 2100 3.917910447761194 0.5530449944372782 ERCC-00111 994 517903 521.0291750503018 50.78025073348398 ERCC-00112 1136 125949 110.8705985915493 10.813011257926474 ERCC-00113 840 5375357 6399.234523809524 625.8343135369684 ERCC-00116 1991 21143 10.619286790557508 2.7410074711485928 ERCC-00117 1136 0 0.0 0.0 ERCC-00120 536 519 0.9682835820895522 0.21549113191719088 ERCC-00123 1022 0 0.0 0.0 ERCC-00126 1118 2206 1.9731663685152057 0.23350913303792836 ERCC-00130 1059 14771799 13948.818696883853 1367.715287711559 ERCC-00131 771 143693 186.3722438391699 23.596797501999312 ERCC-00134 274 526 1.9197080291970803 0.3871710645365216 ERCC-00136 1033 1247900 1208.0348499515974 105.9301059080992 ERCC-00137 537 1042 1.9404096834264433 0.3255172178284071 ERCC-00138 1024 0 0.0 0.0 ERCC-00142 493 973 1.973630831643002 0.23481275515100952 ERCC-00143 784 9993 12.746173469387756 1.4965692275441724 ERCC-00144 538 59181 110.00185873605948 14.900528956629465 ERCC-00145 1042 397170 381.1612284069098 41.26724315696096 ERCC-00147 1023 3042 2.973607038123167 0.25373489696031204 ERCC-00148 494 20651 41.80364372469636 6.0879653928492825 ERCC-00150 743 4056 5.458950201884253 1.0553602178205306 ERCC-00154 537 7895 14.702048417132216 1.8210433923031442 ERCC-00156 494 0 0.0 0.0 ERCC-00157 1019 12416 12.18449460255152 1.3093590387940517 ERCC-00158 1027 1010 0.9834469328140214 0.16887340231299347 ERCC-00160 743 23763 31.98250336473755 3.833389008253601 ERCC-00162 523 90554 173.1434034416826 22.63514633394074 ERCC-00163 543 50051 92.17495395948434 12.109455119989757 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 89151 102.23738532110092 11.047087515271622 ERCC-00168 1024 2009 1.9619140625 0.32571982849873615 ERCC-00170 1023 23451 22.923753665689148 2.5913146983329485 ERCC-00171 505 8899547 17622.865346534654 2567.761656907743 GL000008.2 209709 233219 1.1121077302357076 1.1109015838879877 GL000009.2 201709 4622 0.022914198176581115 0.05609608581211581 GL000194.1 191469 6711683 35.053627480166504 34.8874402407983 GL000195.1 182896 901219 4.927494313708337 4.998691801715568 GL000205.2 185591 678391 3.655301173009467 4.969017324763209 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 1623 0.011784951858144904 0.10679421533177157 GL000216.2 176608 24408 0.13820438485232833 0.14576475508007736 GL000218.1 161147 2044872 12.68948227394863 12.73890078345673 GL000219.1 179198 3147356 17.563566557662472 20.99463574823019 GL000220.1 161802 749422 4.631722722834081 20.590740205078937 GL000221.1 155397 13852 0.08913942997612566 0.2747239946115531 GL000224.1 179693 305634 1.7008675908354804 2.5636387337368194 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 31921 0.08141845274077249 0.0945594056738883 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 23533 0.13443203564593983 0.15460438384063255 KI270707.1 32032 0 0.0 0.0 KI270708.1 127682 26532 0.20779749690637678 0.2113139963404204 KI270709.1 66860 0 0.0 0.0 KI270710.1 40176 0 0.0 0.0 KI270711.1 42210 13859 0.3283345178867567 1.5375103465265452 KI270712.1 176043 71409 0.40563385082053816 0.9380217405974001 KI270713.1 40745 16395 0.402380660203706 1.9532791980172652 KI270714.1 41717 5959 0.1428434451182971 0.1746617292480931 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 12080 0.3015326244321302 0.3062115655187981 KI270718.1 38054 17335 0.4555368686603248 0.5084488361268514 KI270719.1 176845 149 8.425457321383132E-4 0.02881918748700656 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 124597 1.2420451373659236 1.45748253791746 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 55137 0.12300556834609412 0.21169395796850377 KI270728.1 1872759 21278 0.011361846345418711 0.06654272566385173 KI270729.1 280839 1303 0.0046396689918423014 0.024424260171729162 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 6089 0.04039030473486607 0.5209198240628213 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 1136727 6.323159335157866 21.512379567525898 KI270734.1 165050 3519631 21.324634959103303 62.459797177622626 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 221 0.0022238993710691824 0.04710577079994064 KI270739.1 73985 0 0.0 0.0 KI270740.1 37240 0 0.0 0.0 KI270741.1 157432 333892 2.120864881345597 2.6316387035485205 KI270742.1 186739 4117413 22.049025645419544 21.991313889553034 KI270743.1 210658 3180646 15.098624310493786 15.067478679909408 KI270744.1 168472 1913 0.011355002611709958 0.1661786713200757 KI270745.1 41891 1159 0.027667040653123583 0.195903998602704 KI270746.1 66486 26191 0.39393255723009357 0.3959603212257959 KI270747.1 198735 0 0.0 0.0 KI270748.1 93321 19088 0.20454131438797268 0.3769425565741409 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 76728 2.765471256082177 2.7406415506833346 KI270753.1 62944 0 0.0 0.0 KI270754.1 40191 0 0.0 0.0 KI270755.1 36723 2484 0.06764153255452986 0.27076985766034967 KI270756.1 79590 0 0.0 0.0 KI270757.1 71251 0 0.0 0.0 SIRVome_isoforms 231019 1112551451 4815.843939243093 4860.542034220473