BamQC report ----------------------------------- >>>>>>> Input bam file = output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep3.bam outfile = output/mappings/longReadMapping/bamqc/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep3/genome_results.txt >>>>>>> Reference number of bases = 3,110,632,377 bp number of contigs = 288 >>>>>>> Globals number of windows = 687 number of reads = 12,416,052 number of mapped reads = 12,416,052 (100%) number of secondary alignments = 0 number of mapped bases = 97,185,467,454 bp number of sequenced bases = 7,292,548,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,502,821 duplication rate = 36.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 5.855 >>>>>>> ACTG content number of A's = 1,839,626,193 bp (25.23%) number of C's = 1,784,780,232 bp (24.47%) number of T's = 1,864,323,474 bp (25.56%) number of G's = 1,803,818,645 bp (24.74%) number of N's = 0 bp (0%) GC percentage = 49.21% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 248,677,335 number of insertions = 50,254,993 mapped reads with insertion percentage = 89.81% number of deletions = 79,904,469 mapped reads with deletion percentage = 95.23% homopolymer indels = 33.89% >>>>>>> Coverage mean coverageData = 31.243X std coverageData = 267.1754X There is a 2.65% of reference with a coverageData >= 1X There is a 1.56% of reference with a coverageData >= 2X There is a 1.16% 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 0.64% 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 0.5% 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 0.24% 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 0.23% 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 0.22% 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 0.21% 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 9448813640 37.95368508308655 183.68489600194297 chr10 133797422 2836111022 21.197052825128424 123.236570272494 chr11 135086622 4502077630 33.32733888334257 288.4948740173848 chr12 133275309 4368169606 32.775535384427435 199.66510643962792 chr13 114364328 1490602569 13.033806913988075 117.72132919615693 chr14 107043718 4562540053 42.623146301775506 427.3256343988382 chr15 101991189 2664073825 26.120627194570698 281.0394668773787 chr16 90338345 2897769901 32.076853976016494 372.33446478932836 chr17 83257441 3875204836 46.544846796336195 326.61511739009813 chr18 80373285 2267370093 28.210494233251758 201.27027390345597 chr19 58617616 6081394523 103.74687573442085 472.45855428184086 chr2 242193529 8553743078 35.3178018971762 467.2092291312867 chr20 64444167 2136775856 33.15700947767701 268.1143299942318 chr21 46709983 3070085661 65.7265420327813 373.80308976018586 chr22 50818468 1645022744 32.370569376471565 192.02958461246192 chr3 198295559 6654791255 33.55996114365829 224.54857527811984 chr4 190214555 3955694249 20.795959851757928 205.42037582106576 chr5 181538259 6352459043 34.992398175417115 222.58669297103484 chr6 170805979 4441969885 26.005939083666387 237.1229409393883 chr7 159345973 5008291877 31.430300890001156 261.70858701166685 chr8 145138636 4830729131 33.28355057022859 183.81797273525225 chr9 138394717 2740484162 19.801942020662537 208.03158984596922 chrIS 10567884 0 0.0 0.0 chrM 16569 53801287 3247.1052568048767 3470.5361312683503 chrX 156040895 2529466121 16.210276934133198 158.69140698135374 chrY 57227415 167007252 2.9183085065086374 11.399323147501256 ERCC-00002 1061 1213176 1143.4269557021678 381.70436392038005 ERCC-00003 1023 21507 21.023460410557185 5.722478233874277 ERCC-00004 523 161914 309.5869980879541 57.270049796190165 ERCC-00009 984 42192 42.8780487804878 9.158364726175941 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 3158 4.903726708074534 0.6115174169021873 ERCC-00022 751 4581 6.099866844207723 1.5041318610071088 ERCC-00024 536 0 0.0 0.0 ERCC-00025 1994 1431 0.7176529588766299 0.9024530175584556 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 0 0.0 0.0 ERCC-00035 1130 1825 1.6150442477876106 0.8587650927540388 ERCC-00039 740 0 0.0 0.0 ERCC-00040 744 730 0.9811827956989247 0.19788671341698605 ERCC-00041 1122 0 0.0 0.0 ERCC-00042 1023 5113 4.998044965786901 3.248200064136952 ERCC-00043 1023 10835 10.591397849462366 1.515667934570119 ERCC-00044 1156 3634 3.143598615916955 2.012097338005541 ERCC-00046 522 333824 639.5095785440614 89.03856927123319 ERCC-00048 992 0 0.0 0.0 ERCC-00051 274 0 0.0 0.0 ERCC-00053 1023 2288 2.236559139784946 0.9645107346920035 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 525 502 0.9561904761904761 0.22873010365376104 ERCC-00060 523 28065 53.66156787762906 8.328353043375806 ERCC-00061 1136 0 0.0 0.0 ERCC-00062 1023 3898 3.8103616813294234 1.7870328136373685 ERCC-00067 644 0 0.0 0.0 ERCC-00069 1137 1316 1.1574318381706246 0.979614993788263 ERCC-00071 642 5543 8.633956386292835 1.1346419224558757 ERCC-00073 603 0 0.0 0.0 ERCC-00074 522 1074434 2058.302681992337 291.01712635050063 ERCC-00075 1023 0 0.0 0.0 ERCC-00076 642 9883 15.394080996884735 2.189832285144014 ERCC-00077 273 0 0.0 0.0 ERCC-00078 993 377 0.3796576032225579 0.4850518797758227 ERCC-00079 644 5086 7.89751552795031 1.3936212131152572 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 844 720 0.8530805687203792 0.39108142092472575 ERCC-00086 1020 0 0.0 0.0 ERCC-00092 1124 15822 14.076512455516013 4.909483548233564 ERCC-00095 521 1807 3.468330134357006 1.5142652394145117 ERCC-00096 1107 1205666 1089.1291779584462 318.2301450812337 ERCC-00097 523 0 0.0 0.0 ERCC-00098 1143 0 0.0 0.0 ERCC-00099 1350 0 0.0 0.0 ERCC-00104 2022 0 0.0 0.0 ERCC-00108 1022 23791 23.27886497064579 8.333931993411547 ERCC-00109 536 0 0.0 0.0 ERCC-00111 994 16672 16.772635814889338 6.879973576375763 ERCC-00112 1136 3516 3.0950704225352115 1.689823547094024 ERCC-00113 840 124637 148.37738095238095 25.141481208969097 ERCC-00116 1991 6715 3.372677046710196 1.4383220397434404 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 753360 711.3881019830028 310.6599799133859 ERCC-00131 771 3595 4.662775616083009 2.2724283228713373 ERCC-00134 274 0 0.0 0.0 ERCC-00136 1033 39014 37.767666989351405 11.785271396536455 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 2070 3.8475836431226766 0.6997542641399231 ERCC-00145 1042 24530 23.54126679462572 10.68907225320105 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 2167 4.1434034416826 1.4677502409811019 ERCC-00163 543 0 0.0 0.0 ERCC-00164 1022 0 0.0 0.0 ERCC-00165 872 3865 4.432339449541284 1.7994559090099063 ERCC-00168 1024 0 0.0 0.0 ERCC-00170 1023 0 0.0 0.0 ERCC-00171 505 158365 313.5940594059406 50.35675081566051 GL000008.2 209709 0 0.0 0.0 GL000009.2 201709 115221 0.5712238918441914 0.5706361372528712 GL000194.1 191469 6896513 36.01895345982901 35.82819079058748 GL000195.1 182896 1354036 7.403311171376083 7.305969916083727 GL000205.2 185591 536451 2.8905011557672515 4.013121955575606 GL000208.1 92689 0 0.0 0.0 GL000213.1 164239 0 0.0 0.0 GL000214.1 137718 1816 0.01318636634281648 0.15581003937686547 GL000216.2 176608 19128 0.10830766443196231 0.1177837245159799 GL000218.1 161147 2891662 17.944249660248097 17.970337043930662 GL000219.1 179198 3334851 18.60986729762609 22.485624550967856 GL000220.1 161802 773729 4.781949543268934 13.223816046307395 GL000221.1 155397 259702 1.6712163040470536 1.6682548213531005 GL000224.1 179693 360125 2.0041125697717774 3.768754701327052 GL000225.1 211173 241 0.0011412443825678472 0.03355246649769793 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 1133 0.010070663526065508 0.09975884084452817 KI270442.1 392061 63583 0.16217629399506708 0.18550414605635895 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 331 0.0018908343092171032 0.0433770465478869 KI270707.1 32032 0 0.0 0.0 KI270708.1 127682 0 0.0 0.0 KI270709.1 66860 5350 0.08001794795094226 0.11646372138030166 KI270710.1 40176 0 0.0 0.0 KI270711.1 42210 19590 0.4641080312722104 1.3297118016748668 KI270712.1 176043 37078 0.2106189964951745 0.7943427988434983 KI270713.1 40745 19505 0.4787090440544852 2.5216683639038453 KI270714.1 41717 11498 0.2756190521849606 0.31746281615670635 KI270715.1 161471 0 0.0 0.0 KI270716.1 153799 0 0.0 0.0 KI270717.1 40062 36574 0.9129349508262193 0.9241762919663216 KI270718.1 38054 3351 0.08805907394754822 0.1707900360793242 KI270719.1 176845 20906 0.11821651728915152 0.12779913683630562 KI270720.1 39050 0 0.0 0.0 KI270721.1 100316 125103 1.247089198133897 1.3601363891638822 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 8940 0.05173311729645275 0.06725499330792721 KI270726.1 43739 0 0.0 0.0 KI270727.1 448248 70461 0.15719200085666862 0.16947169621181463 KI270728.1 1872759 7238 0.003864885978388036 0.04275199675008201 KI270729.1 280839 29196 0.10395992009656778 0.10736325563717174 KI270730.1 112551 0 0.0 0.0 KI270731.1 150754 2128 0.014115711689242076 0.23545272591357305 KI270732.1 41543 0 0.0 0.0 KI270733.1 179772 1135456 6.3160892686291525 16.63856515806742 KI270734.1 165050 4547183 27.550336261738867 76.52772964142075 KI270735.1 42811 0 0.0 0.0 KI270736.1 181920 5214 0.028660949868073878 0.03866636331451803 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 120362 0.764533258803801 1.1684636170680898 KI270742.1 186739 5594201 29.957325464953758 29.893567942287262 KI270743.1 210658 2626116 12.466253358524243 12.439074505865834 KI270744.1 168472 1303 0.007734222897573484 0.09953650080465709 KI270745.1 41891 999 0.023847604497386075 0.15167762262729717 KI270746.1 66486 4786 0.07198507956562283 0.1259186577155149 KI270747.1 198735 913 0.004594057413138099 0.0676236057129675 KI270748.1 93321 9179 0.098359426067016 0.1496631481220742 KI270749.1 158759 0 0.0 0.0 KI270750.1 148850 0 0.0 0.0 KI270751.1 150742 816 0.005413222592243701 0.05661559494095916 KI270752.1 27745 399975 14.41611101099297 14.726690746911979 KI270753.1 62944 0 0.0 0.0 KI270754.1 40191 0 0.0 0.0 KI270755.1 36723 1863 0.050731149415897396 0.25749668926595487 KI270756.1 79590 0 0.0 0.0 KI270757.1 71251 0 0.0 0.0 SIRVome_isoforms 231019 14242725 61.65174725888347 63.21481840638745