BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_haploid_reference_match/alignment/5X_haploid_reference_match.sorted.bam outfile = results/5X_haploid_reference_match/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 = 80,365,282 number of mapped reads = 80,365,282 (100%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,182,641 number of mapped paired reads (second in pair) = 40,182,641 number of mapped paired reads (both in pair) = 80,365,282 number of mapped paired reads (singletons) = 0 number of mapped bases = 12,054,771,866 bp number of sequenced bases = 12,054,771,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,340,044 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 356.1232 std insert size = 15,097.1576 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 32.4445 >>>>>>> ACTG content number of A's = 3,538,317,065 bp (29.35%) number of C's = 2,489,064,330 bp (20.65%) number of T's = 3,538,604,130 bp (29.35%) number of G's = 2,488,765,311 bp (20.65%) number of N's = 21,029 bp (0%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0 number of mismatches = 11,151 number of insertions = 2 mapped reads with insertion percentage = 0% number of deletions = 1 mapped reads with deletion percentage = 0% homopolymer indels = 100% >>>>>>> Coverage mean coverageData = 5X std coverageData = 2.3297X There is a 98.46% of reference with a coverageData >= 1X There is a 94.99% of reference with a coverageData >= 2X There is a 86.64% of reference with a coverageData >= 3X There is a 72.93% of reference with a coverageData >= 4X There is a 55.88% of reference with a coverageData >= 5X There is a 38.81% of reference with a coverageData >= 6X There is a 24.45% of reference with a coverageData >= 7X There is a 14.04% of reference with a coverageData >= 8X There is a 7.39% of reference with a coverageData >= 9X There is a 3.6% of reference with a coverageData >= 10X There is a 1.63% of reference with a coverageData >= 11X There is a 0.69% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 613735270 5.002782428926077 2.3071348212600262 NC_006584.3 85426708 428304354 5.013705479555644 2.3181753310856354 NC_006585.3 91889043 459690103 5.002665040270362 2.2972352987320215 NC_006586.3 88276631 441642973 5.00294322514415 2.2900148616051115 NC_006587.3 88915250 444686657 5.001241710505228 2.3018970712858864 NC_006588.3 77573801 388003470 5.001733381609082 2.3143910445744136 NC_006589.3 80974532 404915559 5.00052978385846 2.298538722201938 NC_006590.3 74330416 371677079 5.000336322616572 2.2946285824098727 NC_006591.3 61074082 305864340 5.008087391309459 2.3184779612069306 NC_006592.3 69331447 346638736 4.999733180240707 2.310212232936119 NC_006593.3 74389097 372100932 5.002089647626722 2.2931868755666382 NC_006594.3 72498081 362447442 4.99940739121081 2.2851235600914195 NC_006595.3 63241923 316218428 5.0001393537638 2.296429689973812 NC_006596.3 60966679 304890389 5.000934838520563 2.29247624540489 NC_006597.3 64190966 320945069 4.9998479381039385 2.306167587395629 NC_006598.3 59632846 298675018 5.008565547919682 2.315927208902028 NC_006599.3 64289059 321674825 5.003570280908918 2.2942718936863695 NC_006600.3 55844845 279385038 5.002879639114407 2.3104219969905717 NC_006601.3 53741614 268786370 5.001456971500707 2.286245907843079 NC_006602.3 58134056 290674860 5.000078783424298 2.3036189817957733 NC_006603.3 50858623 254327917 5.000684289073261 2.2996877600026493 NC_006604.3 61439934 307204306 5.000075455810222 2.2833863490051853 NC_006605.3 52294480 261450402 4.99957934374718 2.285345962640471 NC_006606.3 47698779 238587531 5.001963069117555 2.3020188506355934 NC_006607.3 51628933 258109904 4.9993267147318345 2.3026623093786744 NC_006608.3 38964690 194998496 5.00449242634806 2.308063866135892 NC_006609.3 45876710 229363066 4.999553498932247 2.2865625443188504 NC_006610.3 41182112 205889344 4.999484824867651 2.3004178861552274 NC_006611.3 41845238 209224589 4.9999617399714635 2.2925579311506414 NC_006612.3 40214260 201057736 4.9996627067115 2.296852174098876 NC_006613.3 39895921 199488776 5.000229873124122 2.2911273266895393 NC_006614.3 38810281 194040149 4.999709973756696 2.2843227759502622 NC_006615.3 31377067 156971687 5.00275207367215 2.2937068498895794 NC_006616.3 42124431 210596331 4.99938695907845 2.2974156112120876 NC_006617.3 26524999 132640910 5.0006000000226205 2.2932510144483986 NC_006618.3 30810995 154062991 5.000260166865757 2.295877012534905 NC_006619.3 30902991 154495901 4.999383425377822 2.3157535513182164 NC_006620.3 23914537 119589231 5.000691880424029 2.313265873829157 NC_006621.3 123869142 619363263 5.000141705994864 2.3084789934616032 NW_003726127.1 2660953 13352361 5.0178868247578965 2.4419373136550675 NW_003726128.1 1881673 9428690 5.01080155797527 2.867175590930215 NW_003726129.1 1415205 7089579 5.009577411046457 2.7380831140669493 NW_003726130.1 1067467 5359751 5.020999244004733 3.0571214053092266 NW_003726131.1 866315 4349700 5.020921951022434 2.310200951458658 NW_003726132.1 881102 4446276 5.046267061021312 2.6562948974483245 NW_003726133.1 822601 4143859 5.037507856178147 2.5915003527310114 NW_003726134.1 741967 3713987 5.005595936207405 2.2594155284187507 NW_003726135.1 745551 3743688 5.02137077141604 3.270235478460296 NW_003726136.1 602611 3009900 4.994764450034931 2.33971691634043 NW_003726137.1 573630 2870665 5.004384359255966 2.4556211208283387 NW_003726138.1 666183 3327288 4.994555550051563 3.2314312088601924 NW_003726139.1 557017 2807674 5.040553519910524 2.6260159888057695 NW_003726140.1 510604 2577286 5.047524108702635 2.3478914916831997 NW_003726141.1 497093 2510993 5.051354575501969 2.4374577285835612 NW_003726142.1 492630 2468995 5.011864888455839 2.5346790471553855 NW_003726143.1 577062 2876250 4.984299780612829 3.508746796469056 NW_003726144.1 561270 2789074 4.969219805084896 3.3640742880437067 NW_003726145.1 407330 2044800 5.020008347040483 2.2785160976879273 NW_003726146.1 405216 2042700 5.041015162283819 2.2323347304424446 NW_003726147.1 508668 2557044 5.026940951661988 3.4907129795634244 NW_003726148.1 540093 2706900 5.011914614705245 4.023990654874847 NW_003726149.1 448434 2235568 4.985277655128737 3.252389895229889 NW_003726150.1 377800 1897045 5.021294335627316 2.4788281307343927 NW_003726151.1 384880 1923000 4.996362502598212 2.728645717271408 NW_003726152.1 367143 1838695 5.00811672835925 2.4652355320864485 NW_003726153.1 399987 2005800 5.014662976546738 3.0137788069372378 NW_003726154.1 376204 1890282 5.024619621269311 2.695542873018813 NW_003726155.1 416178 2074200 4.983925147412886 3.2760487439505557 NW_003726156.1 365470 1824443 4.9920458587572165 2.8803997187974066 NW_003726157.1 322752 1613387 4.998844313900456 2.3636489240730016 NW_003726158.1 320591 1627194 5.075607237882536 2.387252776109166 NW_003726159.1 310270 1554900 5.011441647597254 2.439149131826216 NW_003726160.1 433650 2136587 4.9269848956531765 4.064352380618689 NW_003726161.1 273228 1373700 5.027669199349994 2.298534520668162 NW_003726162.1 281659 1425888 5.0624620551802 2.613188529701094 NW_003726163.1 320442 1609200 5.021813619937461 3.2325120868854818 NW_003726164.1 265648 1333200 5.018671324459435 2.317351735970524 NW_003726165.1 241365 1234193 5.11338843660017 2.418240081578216 NW_003726166.1 234529 1187995 5.065450328104413 2.3639738098031584 NW_003726167.1 252720 1304388 5.161396011396011 2.8177065991929893 NW_003726168.1 254975 1279800 5.019315619178351 2.944484122228489 NW_003726169.1 226053 1139395 5.040388758388519 2.37096868998773 NW_003726170.1 223744 1123788 5.022650886727689 2.4557504191120256 NW_003726171.1 227140 1147200 5.050629567667518 2.4808855965538696 NW_003726172.1 219672 1113600 5.069376160821588 2.4551317161861124 NW_003726173.1 214597 1092300 5.090005918069684 2.338264044637616 NW_003726174.1 386314 1926876 4.987849262517019 5.223562420841204 NW_003726175.1 204342 1029000 5.035675485215961 2.3264073993469268 NW_003726176.1 201724 1015193 5.032584124843846 2.3314541757096583 NW_003726177.1 216332 1085100 5.015901484754914 2.715595373945226 NW_003726178.1 200877 1010400 5.029943696889141 2.299579586078775 NW_003726179.1 310654 1505088 4.844901401559291 4.379447456337682 NW_003726180.1 200932 1000500 4.979296478410607 2.317108084215837 NW_003726181.1 201410 1015500 5.041954222729755 2.40588033777283 NW_003726182.1 292533 1423488 4.866076647762816 4.12203815459739 NW_003726183.1 192561 966300 5.018150092697899 2.3448491968710954 NW_003726184.1 210134 1080293 5.140971951231119 2.842150895577827 NW_003726185.1 197844 999295 5.050923960291947 2.674584714322686 NW_003726186.1 196813 1022693 5.1962675229786655 2.8209897829272395 NW_003726187.1 180359 902700 5.00501777011405 2.2712460314938427 NW_003726188.1 210247 1014873 4.827051039967277 3.1597702940038337 NW_003726189.1 177735 912900 5.136298421807748 2.4426319846920794 NW_003726190.1 172100 882600 5.128413712957583 2.3382354239869505 NW_003726191.1 166866 851400 5.102297652008199 2.4031237525297007 NW_003726192.1 164926 837300 5.0768223324400035 2.34372035888413 NW_003726193.1 157598 791394 5.021599258873843 2.78714873104715 NW_003726194.1 143980 720000 5.0006945409084596 2.383376369372915 NW_003726195.1 141074 714295 5.063264669606022 2.266772210508358 NW_003726196.1 139526 699600 5.014119232257787 2.215501861398512 NW_003726197.1 142260 733200 5.153943483762125 2.5640380263016 NW_003726198.1 138160 699000 5.059351476548929 2.307231208701784 NW_003726199.1 142296 714287 5.0197264856355766 2.502918445737713 NW_003726200.1 133119 666595 5.0075120756616265 2.3534351596424847 NW_003726201.1 129748 648300 4.996608810925794 2.2664220335195586 NW_003726202.1 125962 668700 5.308743906892555 2.494933736191303 NW_003726203.1 127429 638395 5.009809384049157 2.436054473020201 NW_003726204.1 128261 641095 4.998362713529444 2.442131897205747 NW_003726205.1 131872 652787 4.950156212084446 2.675276091471722 NW_003726206.1 133432 687300 5.150938305653816 2.8684067404365505 NW_003726207.1 119670 600000 5.013787916771121 2.252727843156655 NW_003726208.1 144750 703195 4.857996545768566 3.320601022442644 NW_003726209.1 120779 605995 5.017387128557116 2.5359150927499376 NW_003726210.1 115952 590100 5.089174830964537 2.2114254093313166 NW_003726211.1 118237 591895 5.006004888486683 2.549130285507187 NW_003726212.1 111908 561900 5.021088751474426 2.2798817986277227 NW_003726213.1 117332 616200 5.251764224593462 2.75799307412673 NW_003726214.1 111759 558900 5.000939521649263 2.3727351994303 NW_003726215.1 108801 547200 5.029365538919679 2.365370536911212 NW_003726216.1 112014 565500 5.048476083346724 2.5619971305487277 NW_003726217.1 106428 546000 5.130228887134964 2.337770134137025 NW_003726218.1 104912 535795 5.107089751410706 2.293711536961546 NW_003726219.1 104646 523800 5.005446935382145 2.2297788759568506 NW_003726220.1 103248 516300 5.000581125058113 2.438567948671596 NW_003726221.1 129482 623977 4.819025038229252 3.4776572102393724 NW_003726222.1 118473 589776 4.97814691955129 3.234475275912664 NW_003726223.1 99993 507000 5.0703549248447395 2.3306781792627316 NW_003726224.1 109585 551694 5.0343933932563765 2.7289256810234526 NW_003726225.1 124049 589783 4.754435747164427 3.2917549428281303 NW_003726226.1 99658 496200 4.979028276706336 2.395145356289066 NW_003726227.1 101741 507295 4.986141280309806 2.6051160002272233 NW_003726228.1 97365 496500 5.0993683561854874 2.2490487353952044 NW_003726229.1 94395 474600 5.027808676307008 2.3799220236498226 NW_003726230.1 102992 492589 4.7827889544819016 2.7942107846141866 NW_003726231.1 95509 475338 4.976892230051618 2.6052040495667925 NW_003726232.1 92047 451800 4.908362032439949 2.4357642877039556 NW_003726233.1 87753 439500 5.0083757820245465 2.2541575393507176 NW_003726234.1 96536 461978 4.785551504102097 2.9762368000117103 NW_003726235.1 86544 447900 5.175402107598447 2.43044629447256 NW_003726236.1 85476 426900 4.9943843886003085 2.2429670359522835 NW_003726237.1 110512 530386 4.799352106558564 3.7132651699268027 NW_003726238.1 83291 415500 4.9885341753610835 2.258881292665546 NW_003726239.1 82459 416400 5.049782316060103 2.3188427152369897 NW_003726240.1 81605 417900 5.121009742050119 2.515307048046037 NW_003726241.1 82380 428993 5.207489681961641 2.359358843992325 NW_003726242.1 102198 477293 4.670277304839625 3.557954144572185 NW_003726243.1 82108 408288 4.972572709114824 2.3377808688612465 NW_003726244.1 87041 431395 4.956227524959502 2.8048166289579792 NW_003726245.1 79722 400200 5.019944306464966 2.3373517649324413 NW_003726246.1 230124 1132487 4.921203351236724 7.339506115644857 NW_003726247.1 78357 392100 5.004020062023814 2.1674650845493306 NW_003726248.1 256406 1260895 4.917572131697386 7.996236743620561 NW_003726249.1 78050 392400 5.027546444586803 2.3803723758241393 NW_003726250.1 81930 410688 5.012669351885756 2.526463981850856 NW_003726251.1 77100 384000 4.980544747081712 2.3095718524528124 NW_003726252.1 77130 386100 5.005834305717619 2.3506204497811702 NW_003726253.1 79078 391800 4.954601785578796 2.536296667222775 NW_003726254.1 90550 443083 4.893241303147432 3.299145621169218 NW_003726255.1 82767 411589 4.972863580895767 2.904472309957528 NW_003726256.1 89070 416689 4.67821937801729 3.1438446770225457 NW_003726257.1 97802 485700 4.966156111326967 3.6294405578962583 NW_003726258.1 79712 398400 4.997992773986351 2.84008077300945 NW_003726259.1 79581 411600 5.17208881516945 2.8890340831548826 NW_003726260.1 73720 367800 4.989148128052089 2.329559859429628 NW_003726261.1 97799 483288 4.941645620098365 3.8557274718661136 NW_003726262.1 73171 369900 5.055281463967965 2.333971502536361 NW_003726263.1 104732 509995 4.869524118702976 3.9449701243477975 NW_003726264.1 78935 382800 4.849559764363083 2.892733007536166 NW_003726265.1 72992 372300 5.1005589653660675 2.3955890057538847 NW_003726266.1 68721 344100 5.00720303837255 2.311465108787555 NW_003726267.1 73611 366586 4.980043743462255 2.8393847913085732 NW_003726268.1 68272 341400 5.000585891727209 2.281852039686612 NW_003726269.1 79297 396594 5.001374579113964 3.3023312609734314 NW_003726270.1 84443 425400 5.037717750435204 3.4578962387188508 NW_003726271.1 80679 374374 4.640290534091895 3.1273333416812887 NW_003726272.1 68834 345900 5.0251329284946396 2.456260956616625 NW_003726273.1 67496 337495 5.0002222353917265 2.4625649187017404 NW_003726274.1 66523 340800 5.123040151526539 2.348331927949023 NW_003726275.1 67057 337500 5.033031599982105 2.3951656420899163 NW_003726276.1 66195 330300 4.989802855200544 2.246559477853458 NW_003726277.1 87584 418194 4.77477621483376 3.6474299695643215 NW_003726278.1 84679 397195 4.6905962517271105 3.404245887825523 NW_003726279.1 65840 328800 4.993924665856622 2.0973192469164945 NW_003726280.1 65696 335400 5.105333658061373 2.386038359563696 NW_003726281.1 66021 330900 5.0120416231199165 2.445390990088005 NW_003726282.1 67300 341093 5.068246656760772 2.4318758103552596 NW_003726283.1 88153 423300 4.801878552062891 3.8663696273049273 NW_003726284.1 92437 439781 4.7576295206464945 4.031223715963285 NW_003726285.1 70351 350983 4.9890264530710295 2.936152875617812 NW_003726286.1 64646 335845 5.195139683816477 2.5112478244389562 NW_003726287.1 69126 343500 4.969186702543182 2.8053281720273917 NW_003726288.1 227674 1035895 4.549904688282369 7.849679504465699 NW_003726289.1 64123 322200 5.024718119863388 2.6461368387447886 NW_003726290.1 61944 308100 4.973847345989927 2.391516985486774 NW_003726291.1 62414 311700 4.994071842855769 2.3122962577817194 NW_003726292.1 61779 310500 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