BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-Telop_HpreCap_0+_Brain01Rep1.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-Telop_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 = 4,192,021 number of mapped reads = 4,192,021 (100%) number of secondary alignments = 0 number of mapped bases = 32,467,857,661 bp number of sequenced bases = 2,961,696,648 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,742,294 duplication rate = 38.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 5.7122 >>>>>>> ACTG content number of A's = 783,031,597 bp (26.44%) number of C's = 700,926,486 bp (23.67%) number of T's = 795,864,888 bp (26.87%) number of G's = 681,873,677 bp (23.02%) number of N's = 0 bp (0%) GC percentage = 46.69% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 96,463,984 number of insertions = 21,829,417 mapped reads with insertion percentage = 90.76% number of deletions = 32,835,357 mapped reads with deletion percentage = 95.02% homopolymer indels = 35.36% >>>>>>> Coverage mean coverageData = 10.4377X std coverageData = 186.8131X There is a 1.57% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.55% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 248956422 3257445818 13.084401646807086 141.09516169819304 chr10 133797422 937189910 7.004543854365146 32.812370186118116 chr11 135086622 1707588738 12.640694635180084 104.53835144070624 chr12 133275309 1481491037 11.116020274993323 79.59368708707727 chr13 114364328 447699965 3.914681901510408 29.79240834809976 chr14 107043718 1062966190 9.930206179871293 36.4530611284426 chr15 101991189 1236632181 12.124892288489743 85.4197540041506 chr16 90338345 764351884 8.4609905572213 34.957434718091925 chr17 83257441 1590699764 19.10579697014709 77.09383365449517 chr18 80373285 1106240071 13.763778238005328 109.97487422389497 chr19 58617616 1275123479 21.75324699319058 104.72922610644736 chr2 242193529 3115604209 12.864110043997089 47.542523543267684 chr20 64444167 1483780109 23.024273228638364 72.72774883881128 chr21 46709983 731293752 15.65604834409809 67.49970420020703 chr22 50818468 633636022 12.468617157054007 45.19207380019768 chr3 198295559 2433107666 12.270106694623454 48.615986331805175 chr4 190214555 1403924798 7.38074327698004 49.58543537150988 chr5 181538259 1423737743 7.842631910444839 34.06399320370996 chr6 170805979 1083938627 6.346022740808154 74.17246610421648 chr7 159345973 1322610325 8.300243175897517 62.06703068594165 chr8 145138636 1376585541 9.484625038091167 28.66892182894525 chr9 138394717 839676561 6.067258774046989 31.84220723316981 chrIS 10567884 0 0.0 0.0 chrM 16569 715353398 43174.20471965719 64395.42407994378 chrX 156040895 952856250 6.106452093856549 34.57119195095332 chrY 57227415 62321008 1.0890061695080933 5.859335320910401 ERCC-00002 1061 523099 493.0245051837889 131.6386333391474 ERCC-00003 1023 4960 4.848484848484849 2.985499678383942 ERCC-00004 523 19712 37.69024856596558 8.29819853517504 ERCC-00009 984 17418 17.701219512195124 5.197503414239106 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 8787 11.700399467376831 4.849063938070373 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 421 0.41315014720314036 0.48892523366806645 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 34625 33.84652981427175 10.266813447683003 ERCC-00043 1023 1557 1.5219941348973607 0.9576684755140707 ERCC-00044 1156 0 0.0 0.0 ERCC-00046 522 80779 154.74904214559388 18.607380675701222 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 0 0.0 0.0 ERCC-00053 1023 1240 1.2121212121212122 0.9574000358461917 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 525 846 1.6114285714285714 0.5173559150692517 ERCC-00060 523 6005 11.481835564053537 1.716109917979522 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 759 0.7419354838709677 1.2106252396247092 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 357164 684.2222222222222 146.78986611319303 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 3818 5.947040498442368 3.1011025438090045 ERCC-00077 273 0 0.0 0.0 ERCC-00078 993 2108 2.122860020140987 0.3950124581350356 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 3339 2.9706405693950177 0.3402870812690414 ERCC-00095 521 244 0.46833013435700577 0.4986304237292313 ERCC-00096 1107 204591 184.81571815718158 68.99852361318402 ERCC-00097 523 0 0.0 0.0 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 2471 1.8303703703703704 0.5943497097697865 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 1019 0.99706457925636 0.09361185157985541 ERCC-00109 536 0 0.0 0.0 ERCC-00111 994 67291 67.69718309859155 32.80579459458439 ERCC-00112 1136 960 0.8450704225352113 1.3291402360585207 ERCC-00113 840 73294 87.2547619047619 15.495555101097736 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 88605 83.6685552407932 20.842202003425317 ERCC-00131 771 2696 3.496757457846952 1.3205364286899623 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 2066 2.0 0.12445427825741101 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 9368 8.990403071017274 3.6903587522758676 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 523 399 0.762906309751434 0.4334950026191647 ERCC-00163 543 1085 1.9981583793738489 0.1134055566728567 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 3017 3.459862385321101 3.1740241805599974 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 0 0.0 0.0 ERCC-00171 505 24780 49.06930693069307 6.495775436370404 GL000008.2 209709 0 0.0 0.0 GL000009.2 201709 2269 0.011248878334630582 0.02732834110921595 GL000194.1 191469 4747214 24.79364283513258 24.73243826341604 GL000195.1 182896 66293 0.36246282040066485 0.608351186946775 GL000205.2 185591 56707 0.3055482216271263 0.6139689179093284 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 174 0.0010594316818782383 0.03177582402637479 GL000214.1 137718 16697 0.12124050596145747 0.18881839357525368 GL000216.2 176608 21197 0.1200228755209277 0.12271737968366297 GL000218.1 161147 935335 5.804234642903684 5.810161439188682 GL000219.1 179198 2357039 13.153266219489057 14.068960212723386 GL000220.1 161802 104903 0.648341800472182 3.0212722874916156 GL000221.1 155397 0 0.0 0.0 GL000224.1 179693 732026 4.073759133633475 7.741992605374056 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 6696 0.05951735478423181 0.07042462492713397 KI270442.1 392061 127052 0.32406181691114394 0.3657173228366815 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 2023 0.5160714285714286 0.5113066530373268 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 182883 1.0447173745394305 1.050955335129291 KI270707.1 32032 2978 0.09296953046953046 0.6002773165513677 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 11566 0.2740108978914949 0.7802986639242517 KI270712.1 176043 46283 0.2629073578614316 0.628798785047162 KI270713.1 40745 1691 0.04150202478831758 0.2290186844685839 KI270714.1 41717 16837 0.403600450655608 0.5656561781724324 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 778 0.019419899156307725 0.2599949269217768 KI270718.1 38054 1160 0.030482997845167392 0.2656108397856827 KI270719.1 176845 422 0.0023862704628346857 0.04855991605535881 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 42455 0.4232126480322182 0.6418676761553259 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 898 0.0020033552854669735 0.08507441799429812 KI270728.1 1872759 159565 0.08520316815991806 0.09419890389455243 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 302929 1.6850733150880004 3.246820573820198 KI270734.1 165050 239385 1.4503786731293546 3.6772711618851446 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 232 0.0023345911949685535 0.0480531899432675 KI270739.1 73985 0 0.0 0.0 KI270740.1 37240 0 0.0 0.0 KI270741.1 157432 195613 1.2425237562884293 1.6900618247009118 KI270742.1 186739 801285 4.290935476788459 4.280903654538963 KI270743.1 210658 0 0.0 0.0 KI270744.1 168472 512 0.0030390806780948762 0.08863797610135282 KI270745.1 41891 1167 0.027858012460910457 0.3274606215393816 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 8544 0.05667962478937522 0.11696761804335276 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 9261284 40.088841177565484 41.27254159177923