BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep2.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep2/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 9,796,279 number of mapped reads = 9,796,279 (100%) number of secondary alignments = 0 number of mapped bases = 91,024,562,861 bp number of sequenced bases = 6,417,938,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,920,590 duplication rate = 37.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.3759 >>>>>>> ACTG content number of A's = 1,603,208,412 bp (24.98%) number of C's = 1,593,065,262 bp (24.82%) number of T's = 1,606,130,438 bp (25.03%) number of G's = 1,615,534,041 bp (25.17%) number of N's = 0 bp (0%) GC percentage = 49.99% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 258,101,886 number of insertions = 49,820,726 mapped reads with insertion percentage = 92.87% number of deletions = 86,730,715 mapped reads with deletion percentage = 97.39% homopolymer indels = 34.39% >>>>>>> Coverage mean coverageData = 29.2624X std coverageData = 199.728X There is a 2.5% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 1.12% of reference with a coverageData >= 3X There is a 0.92% of reference with a coverageData >= 4X There is a 0.79% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.64% of reference with a coverageData >= 7X There is a 0.59% of reference with a coverageData >= 8X There is a 0.55% of reference with a coverageData >= 9X There is a 0.52% of reference with a coverageData >= 10X There is a 0.49% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.44% 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 0.37% of reference with a coverageData >= 17X There is a 0.36% of reference with a coverageData >= 18X There is a 0.35% of reference with a coverageData >= 19X There is a 0.34% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.32% of reference with a coverageData >= 22X There is a 0.31% of reference with a coverageData >= 23X There is a 0.3% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 8493092280 34.11477483396673 152.94094924247526 chr10 133797422 2682682962 20.050333720181843 103.14093824148928 chr11 135086622 4448829856 32.933163848008576 253.6569100365047 chr12 133275309 4921490403 36.927248114652656 172.56791113720072 chr13 114364328 1376263409 12.034026982609472 93.73211939880012 chr14 107043718 3953875255 36.93701348265949 352.3572869675349 chr15 101991189 2577598242 25.272754119966187 198.13005854078813 chr16 90338345 2757529653 30.52446503198614 281.38007463859424 chr17 83257441 3443929887 41.36482992553182 248.26606182996048 chr18 80373285 2625832059 32.67045833699593 224.08257947372798 chr19 58617616 5213096537 88.93395693540317 378.99869269490654 chr2 242193529 7911262220 32.665043746895485 272.6226315670523 chr20 64444167 2183092691 33.87572208047937 156.86009815984335 chr21 46709983 2454401129 52.5455367645927 317.66155447033157 chr22 50818468 1559363844 30.684983341095602 159.74241948182544 chr3 198295559 6295747899 31.749313654573577 159.66065016740794 chr4 190214555 3621113837 19.036996601022462 128.58800586546508 chr5 181538259 5663882477 31.19938743601149 156.4507276367177 chr6 170805979 4176429143 24.451305319938477 177.73560993111673 chr7 159345973 4524634628 28.39503592600988 193.09747691043515 chr8 145138636 4055573949 27.942759149259196 111.93013833363533 chr9 138394717 2597638440 18.769780352237 179.52614495978037 chrIS 10567884 0 0.0 0.0 chrM 16569 27299049 1647.5978634799928 1396.7511664910544 chrX 156040895 2941179498 18.84877357310723 157.11861584431242 chrY 57227415 153312014 2.678995967230042 11.62165741667072 ERCC-00002 1061 32697695 30817.80867106503 3369.1792640479907 ERCC-00003 1023 6051 5.914956011730205 0.9502311005979255 ERCC-00004 523 99737 190.7017208413002 27.264522804535225 ERCC-00009 984 1080272 1097.8373983739837 111.99979772155255 ERCC-00012 994 0 0.0 0.0 ERCC-00013 808 806 0.9975247524752475 0.0859948156734665 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 44857 69.65372670807453 8.83791035735185 ERCC-00022 751 124348 165.57656458055925 19.947721393914605 ERCC-00024 536 523 0.9757462686567164 0.185247196266665 ERCC-00025 1994 3331 1.6705115346038115 0.9763226447165707 ERCC-00028 1130 0 0.0 0.0 ERCC-00031 1138 1124 0.9876977152899824 0.23816140058326787 ERCC-00033 2022 0 0.0 0.0 ERCC-00034 1019 13722 13.466143277723258 1.7803321713472793 ERCC-00035 1130 27573 24.40088495575221 2.229139600062466 ERCC-00039 740 2187 2.9554054054054055 0.43492734672824107 ERCC-00040 744 0 0.0 0.0 ERCC-00041 1122 0 0.0 0.0 ERCC-00042 1023 9138 8.932551319648093 1.276388821038031 ERCC-00043 1023 97233 95.04692082111437 8.937202781911848 ERCC-00044 1156 16746 14.486159169550174 1.7097829098127464 ERCC-00046 522 766897 1469.1513409961685 194.43950076760837 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 3420 12.481751824817518 2.2330398668017537 ERCC-00057 1021 0 0.0 0.0 ERCC-00058 1136 0 0.0 0.0 ERCC-00059 525 32835 62.542857142857144 8.429607684482443 ERCC-00060 523 2899 5.54302103250478 0.9922283915478355 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 39430 38.54349951124145 3.821301165979053 ERCC-00067 644 3152 4.894409937888199 0.6816045038468912 ERCC-00069 1137 1126 0.990325417766051 0.1316943140825262 ERCC-00071 642 79492 123.81931464174455 13.276072381671058 ERCC-00073 603 592 0.9817578772802653 0.20069761093423674 ERCC-00074 522 559627 1072.0823754789271 140.639380340726 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 278761 434.2071651090343 51.354752430889754 ERCC-00077 273 0 0.0 0.0 ERCC-00078 993 28850 29.05337361530715 4.240045624185496 ERCC-00079 644 92489 143.6164596273292 17.590622263271957 ERCC-00081 534 521 0.9756554307116105 0.194945529176131 ERCC-00083 1022 0 0.0 0.0 ERCC-00084 994 11831 11.90241448692153 3.240474514113119 ERCC-00085 844 4150 4.9170616113744074 0.665176471397722 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 257684 229.25622775800713 25.80818384867376 ERCC-00095 521 505 0.9692898272552783 0.3564377459747703 ERCC-00096 1107 21064863 19028.783197831977 1919.441931990392 ERCC-00097 523 1539 2.94263862332696 0.4640169414737325 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 10081 7.467407407407407 1.103583637516044 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 507239 496.31996086105676 52.76954220914338 ERCC-00109 536 1578 2.9440298507462686 0.37566307309412855 ERCC-00111 994 351668 353.7907444668008 34.23370994607171 ERCC-00112 1136 73705 64.88116197183099 6.085072029002173 ERCC-00113 840 4150362 4940.907142857143 507.865771961385 ERCC-00116 1991 5313 2.6685082872928176 0.9268214974208627 ERCC-00117 1136 0 0.0 0.0 ERCC-00120 536 1579 2.9458955223880596 0.42302227450994406 ERCC-00123 1022 0 0.0 0.0 ERCC-00126 1118 2212 1.9785330948121647 0.37549403795928665 ERCC-00130 1059 9838244 9290.126534466477 937.6230177329082 ERCC-00131 771 123225 159.82490272373542 17.938331199514224 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 826348 799.9496611810262 72.42404929309082 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 1549 1.975765306122449 0.30070406674325906 ERCC-00144 538 35410 65.817843866171 9.460185768354105 ERCC-00145 1042 280140 268.8483685220729 30.351182055365214 ERCC-00147 1023 0 0.0 0.0 ERCC-00148 494 8752 17.7165991902834 2.4331916441464974 ERCC-00150 743 1462 1.9676985195154777 0.3316122551108064 ERCC-00154 537 4226 7.8696461824953445 0.9206376965623018 ERCC-00156 494 484 0.979757085020243 0.22563359988814224 ERCC-00157 1019 6044 5.931305201177625 0.6668509861942241 ERCC-00158 1027 0 0.0 0.0 ERCC-00160 743 10739 14.4535666218035 1.9578905604431325 ERCC-00162 523 0 0.0 0.0 ERCC-00163 543 26588 48.96500920810313 6.553392183924888 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 85225 97.73509174311927 10.578755618601653 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 13132 12.836754643206255 1.3696811194848952 ERCC-00171 505 4461209 8834.077227722772 1337.263759110827 GL000008.2 209709 123 5.86527044618972E-4 0.023914311073930935 GL000009.2 201709 2238 0.011095191587881552 0.0251416768484042 GL000194.1 191469 8014699 41.85899022818315 41.64808008025426 GL000195.1 182896 977142 5.3426100078733265 5.546157546377423 GL000205.2 185591 467533 2.519157717777263 4.101564061821333 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 3586892 22.258509311374088 22.235920085346926 GL000219.1 179198 4461101 24.89481467427092 28.9075943201824 GL000220.1 161802 732623 4.527898295447522 11.134239608392553 GL000221.1 155397 175028 1.126328050091057 1.1272342642725486 GL000224.1 179693 428879 2.386731814817494 3.994599204131695 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 88892 0.5077946930964554 0.5214511934986134 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 1789 0.0423833214877991 0.3006366577782719 KI270712.1 176043 60803 0.34538720653476707 0.593496331032303 KI270713.1 40745 25262 0.6200024542888698 3.3433911450106706 KI270714.1 41717 37216 0.8921063355466596 1.0195402285576196 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 13481 0.33650341969946584 0.3726434505910055 KI270718.1 38054 350 0.009197456246386713 0.1560619388160061 KI270719.1 176845 964 0.0054511012468545905 0.07044685245364407 KI270720.1 39050 1346 0.034468629961587706 0.07173560624334244 KI270721.1 100316 79769 0.795177239921847 0.8580571901372236 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 39861 0.08892621941425283 0.10492324163494082 KI270728.1 1872759 24489 0.013076428947878504 0.11060526055495853 KI270729.1 280839 0 0.0 0.0 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 2571 0.01705427385011343 0.14093990497364534 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 1059302 5.892474912667156 13.7929720600103 KI270734.1 165050 5360774 32.479697061496516 81.70395484096618 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 242372 1.5395345291935565 1.7930119884032873 KI270742.1 186739 2470669 13.230599928242093 13.190511640020494 KI270743.1 210658 2764292 13.122179076987344 13.098598325296479 KI270744.1 168472 1438 0.008535542998243032 0.1098068206712977 KI270745.1 41891 17693 0.42235802439664843 0.49762806722278813 KI270746.1 66486 0 0.0 0.0 KI270747.1 198735 0 0.0 0.0 KI270748.1 93321 353 0.0037826427063576257 0.0600734117965356 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 313 0.011281311948098756 0.14554595806502038 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 255988723 1108.0851488405715 1303.5995769129067