BamQC report ----------------------------------- >>>>>>> Input bam file = results/0.5X_haploid_hi_error_low_variance/alignment/0.5X_haploid_hi_error_low_variance.sorted.bam outfile = results/0.5X_haploid_hi_error_low_variance/qualimap/genome_results.txt >>>>>>> Reference number of bases = 2,410,976,875 bp number of contigs = 3268 >>>>>>> Globals number of windows = 3667 number of reads = 8,036,542 number of mapped reads = 8,036,511 (100%) number of supplementary alignments = 179 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,018,254 number of mapped paired reads (second in pair) = 4,018,257 number of mapped paired reads (both in pair) = 8,036,486 number of mapped paired reads (singletons) = 25 number of mapped bases = 1,201,444,502 bp number of sequenced bases = 1,201,314,846 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,872 duplication rate = 0.17% >>>>>>> Insert size mean insert size = 484.4475 std insert size = 80,174.1724 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.6296 >>>>>>> ACTG content number of A's = 352,612,882 bp (29.35%) number of C's = 253,215,325 bp (21.08%) number of T's = 347,455,133 bp (28.92%) number of G's = 248,029,423 bp (20.65%) number of N's = 2,083 bp (0%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0499 number of mismatches = 59,832,303 number of insertions = 89,635 mapped reads with insertion percentage = 1.11% number of deletions = 89,207 mapped reads with deletion percentage = 1.1% homopolymer indels = 27.52% >>>>>>> Coverage mean coverageData = 0.4983X std coverageData = 0.7178X There is a 38.72% of reference with a coverageData >= 1X There is a 9.24% of reference with a coverageData >= 2X There is a 1.61% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig NC_006583.3 122678785 61183621 0.49873024908096375 0.7165659482538929 NC_006584.3 85426708 42716799 0.500040326966597 0.7183379663826718 NC_006585.3 91889043 45833596 0.49879283213342424 0.7175089387344419 NC_006586.3 88276631 44024225 0.4987075798123741 0.7168289486075543 NC_006587.3 88915250 44320078 0.49845305501587184 0.7172439647343781 NC_006588.3 77573801 38671752 0.49851562642908265 0.7187805218628639 NC_006589.3 80974532 40382484 0.49870598819885736 0.7172444158122797 NC_006590.3 74330416 37069373 0.49871068930920553 0.7174306332778901 NC_006591.3 61074082 30485944 0.49916336032688957 0.7181072777216768 NC_006592.3 69331447 34555090 0.4984042811049364 0.7165068873121379 NC_006593.3 74389097 37082245 0.4984903231181849 0.7168215248179679 NC_006594.3 72498081 36113646 0.49813244022279707 0.7155322818814879 NC_006595.3 63241923 31514175 0.4983114602634711 0.7148246417782966 NC_006596.3 60966679 30383136 0.49835642187431595 0.7178828897211307 NC_006597.3 64190966 31982474 0.4982394874693115 0.7161559700212065 NC_006598.3 59632846 29756231 0.4989906233889961 0.7186223068598678 NC_006599.3 64289059 32054498 0.49859958286214767 0.7171335204942728 NC_006600.3 55844845 27840708 0.49853675840625933 0.7180304896758564 NC_006601.3 53741614 26779744 0.49830554028392227 0.7152366754238173 NC_006602.3 58134056 28969404 0.49832070894898506 0.7165835983220145 NC_006603.3 50858623 25354745 0.498533847446086 0.7171491864191406 NC_006604.3 61439934 30615731 0.4983034486983661 0.7173886496688915 NC_006605.3 52294480 26053069 0.4981992172022745 0.7177852828039525 NC_006606.3 47698779 23783090 0.4986100377957264 0.7158938556631848 NC_006607.3 51628933 25726803 0.4983020470324266 0.7168584995641694 NC_006608.3 38964690 19427669 0.49859678082900183 0.7163242031190374 NC_006609.3 45876710 22861953 0.49833462338515555 0.7179023407135631 NC_006610.3 41182112 20528103 0.4984713508622384 0.7172863518108187 NC_006611.3 41845238 20845677 0.4981612722575505 0.7158282843642939 NC_006612.3 40214260 20030150 0.49808575366051744 0.7147519200440288 NC_006613.3 39895921 19883211 0.498377039597607 0.7179833855619957 NC_006614.3 38810281 19325716 0.4979535190688261 0.7157886139180447 NC_006615.3 31377067 15635459 0.4983084939073496 0.7138316109688866 NC_006616.3 42124431 20990599 0.49829988208030634 0.7172576031593997 NC_006617.3 26524999 13214778 0.49820088588881756 0.7163379801418965 NC_006618.3 30810995 15353856 0.4983239262477567 0.7171759979393478 NC_006619.3 30902991 15392699 0.49809738481301047 0.7166202957995199 NC_006620.3 23914537 11920685 0.49847024008869584 0.7183947210244997 NC_006621.3 123869142 61741902 0.4984445762932628 0.718005956590543 NW_003726127.1 2660953 1329586 0.499665345460818 0.7202822771500254 NW_003726128.1 1881673 941876 0.5005524339244917 0.7416634512315831 NW_003726129.1 1415205 698644 0.4936698216866108 0.7345366846738025 NW_003726130.1 1067467 534175 0.5004135959238084 0.7548074923020339 NW_003726131.1 866315 432171 0.49886126870711 0.7118786950062035 NW_003726132.1 881102 441730 0.501338097064812 0.723715828891564 NW_003726133.1 822601 407526 0.49541150569960407 0.7336598515442843 NW_003726134.1 741967 368465 0.49660564418633174 0.7244071835241994 NW_003726135.1 745551 369112 0.49508618458026343 0.7480506112163048 NW_003726136.1 602611 306175 0.5080806689555949 0.7338321478787408 NW_003726137.1 573630 287607 0.5013806809267298 0.7099528435513002 NW_003726138.1 666183 328697 0.49340346421328674 0.7290776304089268 NW_003726139.1 557017 279266 0.501359922587641 0.744974665274596 NW_003726140.1 510604 251593 0.49273605377161167 0.7146140860478812 NW_003726141.1 497093 251605 0.5061527722176735 0.7178647009490388 NW_003726142.1 492630 245748 0.49884903477254733 0.7209035873988364 NW_003726143.1 577062 287872 0.4988580083249287 0.7703426819778879 NW_003726144.1 561270 275510 0.49086892226557627 0.7458975576645226 NW_003726145.1 407330 205219 0.5038150885031792 0.717100629448058 NW_003726146.1 405216 202729 0.5002986061754718 0.7287656751029763 NW_003726147.1 508668 255538 0.5023669662726965 0.7582644538586789 NW_003726148.1 540093 264657 0.490021163021924 0.7880016945345324 NW_003726149.1 448434 224138 0.49982383137763864 0.7723133301599496 NW_003726150.1 377800 186570 0.49383271572260456 0.7258289101966772 NW_003726151.1 384880 192327 0.49970640199542715 0.738892583865482 NW_003726152.1 367143 188817 0.5142873485263235 0.7171782489123331 NW_003726153.1 399987 200982 0.5024713303182353 0.7396544689640984 NW_003726154.1 376204 189562 0.5038808731432945 0.7416652657064258 NW_003726155.1 416178 205556 0.49391366194272646 0.7373290514191487 NW_003726156.1 365470 181421 0.49640462965496485 0.7233003589820693 NW_003726157.1 322752 161091 0.49911696906603215 0.7337363827821413 NW_003726158.1 320591 160718 0.5013178785430658 0.7010723273670847 NW_003726159.1 310270 153679 0.49530731298546427 0.7037703774607688 NW_003726160.1 433650 212603 0.49026403781851724 0.7995891446560388 NW_003726161.1 273228 135465 0.4957947208924415 0.6925048583059443 NW_003726162.1 281659 138128 0.49040861467235203 0.7150630841492776 NW_003726163.1 320442 161777 0.5048557929360071 0.7511858718340512 NW_003726164.1 265648 133044 0.5008281635848943 0.7167036264149705 NW_003726165.1 241365 125078 0.518211008224059 0.7250739179755105 NW_003726166.1 234529 117779 0.5021937585543792 0.7230178171420554 NW_003726167.1 252720 131834 0.5216603355492244 0.7799986042527384 NW_003726168.1 254975 125592 0.49256593783704283 0.7559376657996993 NW_003726169.1 226053 111324 0.4924685803771682 0.7014969319382072 NW_003726170.1 223744 118817 0.5310399385011442 0.7369736169090019 NW_003726171.1 227140 112039 0.4932596636435678 0.7251038463741701 NW_003726172.1 219672 112702 0.5130467242069995 0.7418139234940005 NW_003726173.1 214597 110026 0.5127098701286598 0.7315054061389796 NW_003726174.1 386314 192361 0.4979394999922343 0.8594986837830068 NW_003726175.1 204342 101065 0.49458750526078826 0.7349492970387785 NW_003726176.1 201724 98751 0.4895352065197993 0.7008416449586289 NW_003726177.1 216332 106986 0.4945454209270935 0.722531309395487 NW_003726178.1 200877 102423 0.5098791797965919 0.7350646279859783 NW_003726179.1 310654 144913 0.4664771739620285 0.7811944397165852 NW_003726180.1 200932 100529 0.5003135389086856 0.7201860584000932 NW_003726181.1 201410 101637 0.504627376992205 0.7178151855800061 NW_003726182.1 292533 140375 0.47986039181904266 0.775515199160441 NW_003726183.1 192561 97139 0.5044583274910288 0.6931995191972894 NW_003726184.1 210134 106701 0.5077759905584056 0.7444417562125415 NW_003726185.1 197844 100426 0.5076019490103314 0.7601899037283905 NW_003726186.1 196813 98892 0.5024668085949607 0.7391662289927744 NW_003726187.1 180359 93382 0.5177562528069017 0.7330615048413355 NW_003726188.1 210247 101322 0.48191888588184373 0.7496212096781462 NW_003726189.1 177735 85781 0.4826342588685402 0.7005603200042942 NW_003726190.1 172100 88496 0.5142126670540383 0.7170073064156189 NW_003726191.1 166866 80923 0.4849579902436686 0.7138351954049715 NW_003726192.1 164926 82556 0.5005638892594254 0.7185914830718416 NW_003726193.1 157598 79441 0.5040736557570528 0.7379661249050591 NW_003726194.1 143980 71806 0.4987220447284345 0.703377994675739 NW_003726195.1 141074 70253 0.49798687213802684 0.7395869604611855 NW_003726196.1 139526 72216 0.5175809526539856 0.7044328258578622 NW_003726197.1 142260 71005 0.4991213271474765 0.7364353771896079 NW_003726198.1 138160 70186 0.5080052113491604 0.7328593846664783 NW_003726199.1 142296 69694 0.48978186315848654 0.7031249215066855 NW_003726200.1 133119 66363 0.49852387713249047 0.7146617936978773 NW_003726201.1 129748 64902 0.5002158029410858 0.7154233587714504 NW_003726202.1 125962 62861 0.4990473317349677 0.7153410949518058 NW_003726203.1 127429 64284 0.5044691553727958 0.7157452231714126 NW_003726204.1 128261 64686 0.504331012544733 0.7158862409025805 NW_003726205.1 131872 64783 0.491256673137588 0.7444075039460016 NW_003726206.1 133432 66647 0.49948288266682656 0.7076574966489108 NW_003726207.1 119670 55879 0.4669424250020891 0.7048198732699241 NW_003726208.1 144750 66322 0.4581830742659758 0.7192218905928702 NW_003726209.1 120779 59175 0.4899444439844675 0.7309258655595637 NW_003726210.1 115952 54438 0.46948737408582863 0.7078720546291993 NW_003726211.1 118237 59284 0.5013997310486565 0.7087466979316762 NW_003726212.1 111908 55793 0.4985613182256854 0.7060998636143866 NW_003726213.1 117332 64066 0.5460232502642075 0.7779219563375316 NW_003726214.1 111759 55668 0.4981075349636271 0.7094554316164653 NW_003726215.1 108801 58243 0.5353167709855607 0.7379956319257327 NW_003726216.1 112014 59865 0.5344421233060154 0.7534133299849594 NW_003726217.1 106428 56448 0.5303867403314917 0.7486918341830419 NW_003726218.1 104912 54025 0.5149553911849931 0.7099357292916357 NW_003726219.1 104646 52250 0.4993024100300059 0.7189438144769293 NW_003726220.1 103248 49653 0.48091004184100417 0.6940026640747395 NW_003726221.1 129482 60405 0.4665127199147372 0.7217646452293512 NW_003726222.1 118473 59489 0.5021312872975278 0.7193861517198965 NW_003726223.1 99993 51321 0.513245927214905 0.7298274124183696 NW_003726224.1 109585 56478 0.5153807546653283 0.7768986680754804 NW_003726225.1 124049 59180 0.47706954509911403 0.7336290660033222 NW_003726226.1 99658 49061 0.49229364426338074 0.7218772522494686 NW_003726227.1 101741 50869 0.49998525668118066 0.7216956374087588 NW_003726228.1 97365 49801 0.5114877009192215 0.7053913822147062 NW_003726229.1 94395 47463 0.5028126489750516 0.719614825839178 NW_003726230.1 102992 49357 0.4792313966133292 0.7258172473339177 NW_003726231.1 95509 47995 0.5025180873006733 0.7326051856122229 NW_003726232.1 92047 45447 0.49373689528175824 0.7410794814352912 NW_003726233.1 87753 42704 0.4866386334370335 0.6683155991618206 NW_003726234.1 96536 46308 0.47969669346150656 0.706756311940456 NW_003726235.1 86544 45010 0.520082270290257 0.6983547943102725 NW_003726236.1 85476 40983 0.47946792081987927 0.7041463148850401 NW_003726237.1 110512 51955 0.4701299406399305 0.7779518227968545 NW_003726238.1 83291 42039 0.5047243999951976 0.7075089967097795 NW_003726239.1 82459 39314 0.47677027371178404 0.6973863123138991 NW_003726240.1 81605 43078 0.5278843208136756 0.753951656701676 NW_003726241.1 82380 41070 0.49854333576110704 0.7209690022327992 NW_003726242.1 102198 48129 0.4709387659249692 0.7279434971804778 NW_003726243.1 82108 41615 0.5068324645588737 0.6916538127823398 NW_003726244.1 87041 41222 0.4735929044932848 0.6807234901978501 NW_003726245.1 79722 39932 0.500890594816989 0.7157588556326583 NW_003726246.1 230124 112694 0.48970989553458133 0.9890117564329897 NW_003726247.1 78357 38831 0.4955651696721416 0.7337599857351407 NW_003726248.1 256406 125427 0.48917342027877664 1.0384356995506703 NW_003726249.1 78050 40021 0.5127610506085842 0.7071868734831397 NW_003726250.1 81930 40917 0.49941413401684365 0.7105803611596148 NW_003726251.1 77100 38541 0.49988326848249026 0.6575018405530233 NW_003726252.1 77130 36753 0.4765071956437184 0.707019326503172 NW_003726253.1 79078 39505 0.4995700447659273 0.7581843866126157 NW_003726254.1 90550 43984 0.4857426836002209 0.7475711324880971 NW_003726255.1 82767 40352 0.4875373035146858 0.7074078286934096 NW_003726256.1 89070 38272 0.4296845177949927 0.6899700978667777 NW_003726257.1 97802 49052 0.5015439357068363 0.7805342721475275 NW_003726258.1 79712 39796 0.49924729024488157 0.753320869612708 NW_003726259.1 79581 37891 0.4761312373556502 0.6737219000408124 NW_003726260.1 73720 37684 0.5111774281063484 0.7050786318944993 NW_003726261.1 97799 47849 0.4892585813760877 0.7759617280201493 NW_003726262.1 73171 37606 0.5139467821951319 0.7034939461068423 NW_003726263.1 104732 50482 0.48201122865981744 0.7629433953142796 NW_003726264.1 78935 37696 0.4775574840058276 0.7296989026131089 NW_003726265.1 72992 36833 0.5046169443226655 0.7976818814678331 NW_003726266.1 68721 35256 0.513030951237613 0.6847564438252088 NW_003726267.1 73611 35645 0.48423469318444257 0.6898440773362093 NW_003726268.1 68272 34304 0.502460745254277 0.7017797510405798 NW_003726269.1 79297 41615 0.5247991727303681 0.809180429674933 NW_003726270.1 84443 39052 0.4624658053361439 0.7593702916078571 NW_003726271.1 80679 40685 0.5042824031036577 0.755125794535078 NW_003726272.1 68834 33721 0.48988871778481563 0.7035065285150707 NW_003726273.1 67496 33188 0.4917032120421951 0.7046223764241328 NW_003726274.1 66523 32282 0.48527576928280447 0.7053680100028535 NW_003726275.1 67057 33187 0.49490731765512924 0.742133536657621 NW_003726276.1 66195 32277 0.48760480398821665 0.6757653538906615 NW_003726277.1 87584 41036 0.46853306540007306 0.7572929252543031 NW_003726278.1 84679 34999 0.4133138086184296 0.7081032041132982 NW_003726279.1 65840 33526 0.5092041312272175 0.6795316798438416 NW_003726280.1 65696 32333 0.4921608621529469 0.7073856662230659 NW_003726281.1 66021 33786 0.5117462625528241 0.7215437796942356 NW_003726282.1 67300 34268 0.509182763744428 0.7318830690914684 NW_003726283.1 88153 42065 0.4771817181491271 0.7877562242363658 NW_003726284.1 92437 47371 0.5124679511451042 0.7890075856905995 NW_003726285.1 70351 34659 0.4926582422424699 0.7658983263844941 NW_003726286.1 64646 36285 0.5612876280048262 0.7785761831991963 NW_003726287.1 69126 34404 0.4976998524433643 0.7417351721010387 NW_003726288.1 227674 102498 0.45019633335383047 1.0184424682737516 NW_003726289.1 64123 31972 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