BamQC report ----------------------------------- >>>>>>> Input bam file = results/0.5X_haploid_hi_error_med_variance/alignment/0.5X_haploid_hi_error_med_variance.sorted.bam outfile = results/0.5X_haploid_hi_error_med_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 = 8,036,396 (100%) number of supplementary alignments = 331 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,018,200 number of mapped paired reads (second in pair) = 4,018,196 number of mapped paired reads (both in pair) = 8,036,322 number of mapped paired reads (singletons) = 74 number of mapped bases = 1,198,438,882 bp number of sequenced bases = 1,197,257,271 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,228 duplication rate = 0.18% >>>>>>> Insert size mean insert size = 747.1742 std insert size = 137,388.8837 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.249 >>>>>>> ACTG content number of A's = 350,821,577 bp (29.3%) number of C's = 252,856,752 bp (21.12%) number of T's = 345,800,548 bp (28.88%) number of G's = 247,776,431 bp (20.7%) number of N's = 1,963 bp (0%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0582 number of mismatches = 68,582,674 number of insertions = 820,498 mapped reads with insertion percentage = 9.73% number of deletions = 824,927 mapped reads with deletion percentage = 9.78% homopolymer indels = 27.55% >>>>>>> Coverage mean coverageData = 0.4971X std coverageData = 0.7166X There is a 38.62% of reference with a coverageData >= 1X There is a 9.19% of reference with a coverageData >= 2X There is a 1.6% 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 61013744 0.49734551903167284 0.7144892390941578 NC_006584.3 85426708 42570495 0.4983277009808221 0.7168442895869924 NC_006585.3 91889043 45713728 0.4974883458085422 0.7154524630915972 NC_006586.3 88276631 43927577 0.49761274872395167 0.7151536380534762 NC_006587.3 88915250 44201609 0.49712067390014647 0.7148810647437088 NC_006588.3 77573801 38567770 0.4971751996527797 0.715909259080496 NC_006589.3 80974532 40273597 0.4973612814458749 0.7154353248102993 NC_006590.3 74330416 36951121 0.49711979279115026 0.717129218461402 NC_006591.3 61074082 30431645 0.4982742925223174 0.7156217990501881 NC_006592.3 69331447 34476604 0.497272240690433 0.7161051405089568 NC_006593.3 74389097 36977555 0.49708299322412797 0.715614491224363 NC_006594.3 72498081 36033288 0.4970240246772877 0.7145015531131748 NC_006595.3 63241923 31445702 0.4972287449260517 0.7157832225055771 NC_006596.3 60966679 30327336 0.4974411678221804 0.7152811587975899 NC_006597.3 64190966 31911565 0.4971348304682002 0.7164168499721918 NC_006598.3 59632846 29705136 0.4981337969346625 0.7158210223944615 NC_006599.3 64289059 31972366 0.4973220404423714 0.7158976141109535 NC_006600.3 55844845 27777511 0.4974051051623476 0.7170421069027622 NC_006601.3 53741614 26717074 0.497139404856728 0.7163443276943313 NC_006602.3 58134056 28882502 0.49682585367860793 0.716162127388258 NC_006603.3 50858623 25290156 0.4972638759802836 0.7160858344369232 NC_006604.3 61439934 30538950 0.4970537566007151 0.7149211472598276 NC_006605.3 52294480 25983593 0.4968706639783013 0.715535211116765 NC_006606.3 47698779 23719016 0.49726673297025065 0.7138959896880357 NC_006607.3 51628933 25663342 0.4970728719107947 0.71573418469344 NC_006608.3 38964690 19387411 0.4975635889827431 0.7149674329852613 NC_006609.3 45876710 22806022 0.49711546446988025 0.7166559337473962 NC_006610.3 41182112 20476435 0.4972167284669616 0.7163918889488383 NC_006611.3 41845238 20783444 0.49667405404648435 0.7159834835769184 NC_006612.3 40214260 19985730 0.4969811703609615 0.7167268640994935 NC_006613.3 39895921 19825561 0.4969320297180256 0.7153172569051814 NC_006614.3 38810281 19288162 0.4969858888679523 0.7153183195471984 NC_006615.3 31377067 15595045 0.4970204831445845 0.714713487818073 NC_006616.3 42124431 20937464 0.49703850005712835 0.7147244256048767 NC_006617.3 26524999 13188305 0.4972028462658943 0.7184479848123054 NC_006618.3 30810995 15306465 0.49678580649537607 0.7154007272189985 NC_006619.3 30902991 15363301 0.49714608530934756 0.7202128517106355 NC_006620.3 23914537 11892563 0.49729430262438284 0.7166667679608159 NC_006621.3 123869142 61586970 0.49719380473306257 0.7168117305018071 NW_003726127.1 2660953 1326151 0.4983744545657139 0.7320196393481148 NW_003726128.1 1881673 930898 0.4947182640129289 0.7428050292599774 NW_003726129.1 1415205 711470 0.5027328196268385 0.7300491117390794 NW_003726130.1 1067467 529492 0.4960265750604 0.7433914542714828 NW_003726131.1 866315 439950 0.5078406815073039 0.7251835383894057 NW_003726132.1 881102 442590 0.5023141475107309 0.7282811436327618 NW_003726133.1 822601 409542 0.49786226858464794 0.7311969780572514 NW_003726134.1 741967 369580 0.4981084064385613 0.7225489266445246 NW_003726135.1 745551 371739 0.498609753055123 0.7603307920587137 NW_003726136.1 602611 300111 0.49801779257265466 0.7222915212817091 NW_003726137.1 573630 287797 0.501711904886425 0.7324287444436905 NW_003726138.1 666183 331013 0.4968799864301551 0.7492423987412241 NW_003726139.1 557017 279971 0.5026255931147523 0.7348966892894865 NW_003726140.1 510604 252818 0.49513517324580303 0.7290039139656787 NW_003726141.1 497093 255306 0.5135980591156987 0.7311227801244294 NW_003726142.1 492630 245404 0.4981507419361387 0.7231359908471577 NW_003726143.1 577062 278669 0.48290998194301477 0.7418252934659724 NW_003726144.1 561270 275489 0.49083150711778645 0.7474281524789388 NW_003726145.1 407330 203334 0.49918739105884663 0.718423117747649 NW_003726146.1 405216 204959 0.5058018439548291 0.7215291187691445 NW_003726147.1 508668 257581 0.5063833384447223 0.771461274528759 NW_003726148.1 540093 270160 0.5002101489928586 0.7971131377487263 NW_003726149.1 448434 221529 0.4940058068745902 0.7557403912393984 NW_003726150.1 377800 188102 0.49788777130757017 0.7191870582380666 NW_003726151.1 384880 189046 0.491181667013095 0.7068293107919215 NW_003726152.1 367143 182555 0.49723132403450426 0.7168588614920054 NW_003726153.1 399987 201658 0.5041613852450204 0.7432070458680542 NW_003726154.1 376204 191510 0.509058914844074 0.7567964844823722 NW_003726155.1 416178 205315 0.49333458279870634 0.7676478575334365 NW_003726156.1 365470 183469 0.5020083727802556 0.71953448379074 NW_003726157.1 322752 168079 0.5207682678960935 0.7352661152938562 NW_003726158.1 320591 163547 0.5101422061130849 0.7116664129145498 NW_003726159.1 310270 155868 0.5023624585038837 0.7388810321720133 NW_003726160.1 433650 212127 0.4891663784157731 0.7842973456265195 NW_003726161.1 273228 136977 0.5013285607624401 0.7384682261642025 NW_003726162.1 281659 140966 0.5004846285756891 0.7237153239965329 NW_003726163.1 320442 159313 0.49716641389081334 0.7530946530175291 NW_003726164.1 265648 132613 0.49920571583448775 0.7059015824795869 NW_003726165.1 241365 115871 0.4800654610237607 0.7040185802865923 NW_003726166.1 234529 119575 0.5098516601358467 0.7277532824488133 NW_003726167.1 252720 131185 0.5190922760367205 0.7829692527955332 NW_003726168.1 254975 127669 0.5007118344935778 0.7312067909815354 NW_003726169.1 226053 115339 0.5102299018371798 0.7049343440183554 NW_003726170.1 223744 115386 0.5157054490846682 0.7461937260036189 NW_003726171.1 227140 114835 0.505569252443427 0.7277717142529122 NW_003726172.1 219672 108218 0.4926344732146109 0.7312194503098949 NW_003726173.1 214597 109672 0.5110602664529327 0.7172777745521385 NW_003726174.1 386314 191139 0.4947762700808151 0.8408906981890301 NW_003726175.1 204342 101854 0.4984486791751084 0.7042972559038038 NW_003726176.1 201724 104064 0.5158731732466142 0.7209293530290882 NW_003726177.1 216332 107612 0.4974391213505168 0.7489651553591103 NW_003726178.1 200877 99651 0.496079690556908 0.7027318878059463 NW_003726179.1 310654 151651 0.48816689950877823 0.7875075822873631 NW_003726180.1 200932 99596 0.49567017697529514 0.7578028746006152 NW_003726181.1 201410 101281 0.5028598381411052 0.735009086535843 NW_003726182.1 292533 148598 0.5079700409868289 0.805158853272505 NW_003726183.1 192561 95523 0.4960661816255628 0.7144931646160447 NW_003726184.1 210134 107682 0.5124444402143394 0.7317100071238846 NW_003726185.1 197844 97462 0.4926204484341198 0.7176738504259079 NW_003726186.1 196813 104940 0.5331964860044814 0.7502362132464401 NW_003726187.1 180359 86766 0.4810738582493804 0.7180045265999849 NW_003726188.1 210247 96013 0.45666763378312175 0.7193063208788252 NW_003726189.1 177735 92995 0.52322277548035 0.7587008210683127 NW_003726190.1 172100 88548 0.5145148169668797 0.7019046960595844 NW_003726191.1 166866 86274 0.5170256373377441 0.737483914363195 NW_003726192.1 164926 78985 0.4789117543625626 0.719506542864764 NW_003726193.1 157598 77087 0.48913691798119263 0.7505259483838199 NW_003726194.1 143980 71543 0.496895402139186 0.730705042248966 NW_003726195.1 141074 70450 0.49938330238031103 0.7344338900741396 NW_003726196.1 139526 71888 0.515230136318679 0.7227647016398602 NW_003726197.1 142260 72577 0.5101715169408126 0.7315459500334621 NW_003726198.1 138160 67750 0.49037348002316156 0.69316183691378 NW_003726199.1 142296 70727 0.497041378534885 0.7110925582727098 NW_003726200.1 133119 66357 0.49847880467852074 0.7115852825946734 NW_003726201.1 129748 64213 0.494905509140796 0.7076680082830327 NW_003726202.1 125962 68009 0.5399168003048539 0.7364212001503256 NW_003726203.1 127429 62622 0.49142659834103697 0.7247151661390789 NW_003726204.1 128261 62111 0.4842547617748185 0.6935329956624979 NW_003726205.1 131872 66584 0.5049138558602281 0.7224550077515249 NW_003726206.1 133432 66070 0.4951585826488399 0.7395895987035521 NW_003726207.1 119670 64978 0.5429765187599231 0.7436773270176394 NW_003726208.1 144750 70159 0.4846908462867012 0.7466839172021529 NW_003726209.1 120779 61098 0.5058660859917701 0.6987773106800513 NW_003726210.1 115952 61861 0.5335052435490548 0.7291976101914303 NW_003726211.1 118237 52460 0.44368514086115174 0.6703522951465071 NW_003726212.1 111908 56206 0.5022518497337098 0.6826653823005855 NW_003726213.1 117332 56701 0.48325265059830225 0.7478554307630042 NW_003726214.1 111759 55488 0.49649692642203314 0.7076796820471123 NW_003726215.1 108801 58679 0.5393240870947877 0.7257043466950356 NW_003726216.1 112014 55380 0.49440248540361026 0.7159051869998143 NW_003726217.1 106428 52514 0.4934227834780321 0.6977674794869068 NW_003726218.1 104912 52290 0.49841772151898733 0.7256385922054294 NW_003726219.1 104646 51283 0.490061731934331 0.6882560243388014 NW_003726220.1 103248 49496 0.47938943127227646 0.7208082384425238 NW_003726221.1 129482 65864 0.5086730201881342 0.7918163328457103 NW_003726222.1 118473 61143 0.5160922741890558 0.7740628353596052 NW_003726223.1 99993 52783 0.5278669506865481 0.7775796086215205 NW_003726224.1 109585 57253 0.5224528904503354 0.7368774713655788 NW_003726225.1 124049 60930 0.4911768736547655 0.7470373221422338 NW_003726226.1 99658 48399 0.48565092616749284 0.72168602450545 NW_003726227.1 101741 51111 0.5023638454507032 0.7214482871090867 NW_003726228.1 97365 49794 0.5114158065013095 0.7427459315218392 NW_003726229.1 94395 47266 0.5007256740293448 0.7409876777840857 NW_003726230.1 102992 49303 0.4787070840453628 0.7433438031386503 NW_003726231.1 95509 44396 0.46483577463903925 0.670508879093062 NW_003726232.1 92047 47636 0.5175182243853683 0.7284637129453995 NW_003726233.1 87753 42273 0.48172712044032684 0.7107338572932772 NW_003726234.1 96536 47127 0.4881805751222342 0.7311291902506905 NW_003726235.1 86544 44309 0.5119823442410797 0.7098024540144415 NW_003726236.1 85476 43952 0.5142028171650522 0.7139950898913039 NW_003726237.1 110512 51271 0.46394056754017665 0.7449184211429208 NW_003726238.1 83291 43028 0.5165984320034578 0.7135787465674628 NW_003726239.1 82459 43326 0.5254247565456772 0.7483686971001108 NW_003726240.1 81605 41099 0.503633355799277 0.7047978689600968 NW_003726241.1 82380 45803 0.555996601116776 0.7877879467658594 NW_003726242.1 102198 50195 0.49115442572261686 0.7705413497728296 NW_003726243.1 82108 40576 0.49417839918156575 0.7621289790529928 NW_003726244.1 87041 42701 0.4905848967727852 0.6966099550500434 NW_003726245.1 79722 41609 0.5219261935224907 0.7013451602614095 NW_003726246.1 230124 110607 0.48064087187777027 1.0061774786693773 NW_003726247.1 78357 38291 0.48867363477417464 0.6884467274521191 NW_003726248.1 256406 124965 0.4873715903684001 1.040253335756182 NW_003726249.1 78050 39165 0.5017937219730941 0.7460370841313372 NW_003726250.1 81930 38597 0.4710972781642866 0.756792629116788 NW_003726251.1 77100 39141 0.5076653696498055 0.7277633561059358 NW_003726252.1 77130 37582 0.4872552832879554 0.7037264103653461 NW_003726253.1 79078 39918 0.5047927362856927 0.7475899510192552 NW_003726254.1 90550 42049 0.4643732744340144 0.7176677383830959 NW_003726255.1 82767 39048 0.47178223204900505 0.7100626716686789 NW_003726256.1 89070 37529 0.42134276411810934 0.6685421131026736 NW_003726257.1 97802 49056 0.5015848346659577 0.7633960453475884 NW_003726258.1 79712 39769 0.4989085708550783 0.7210542558679052 NW_003726259.1 79581 38662 0.485819479524007 0.7285328863736216 NW_003726260.1 73720 37547 0.5093190450352686 0.7117950459112516 NW_003726261.1 97799 52793 0.5398112455137578 0.8370665342582144 NW_003726262.1 73171 37904 0.5180194339287423 0.7631996243467022 NW_003726263.1 104732 50065 0.47802963755108274 0.733423705849534 NW_003726264.1 78935 37299 0.4725280293912713 0.7390854791649464 NW_003726265.1 72992 35928 0.49221832529592285 0.742612530303417 NW_003726266.1 68721 33571 0.48851151758559974 0.6917920496642719 NW_003726267.1 73611 33806 0.4592520139653041 0.6683288980398797 NW_003726268.1 68272 33981 0.4977296695570659 0.746735409650521 NW_003726269.1 79297 38218 0.481960225481418 0.7462455823577473 NW_003726270.1 84443 37726 0.4467629051549566 0.7201628626423905 NW_003726271.1 80679 39378 0.4880824006246979 0.7463463986764678 NW_003726272.1 68834 35489 0.515573699044077 0.7670812426902591 NW_003726273.1 67496 33408 0.4949626644541899 0.6852494824026398 NW_003726274.1 66523 32516 0.4887933496685357 0.696437862864939 NW_003726275.1 67057 33400 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