BamQC report ----------------------------------- >>>>>>> Input bam file = results/0.5X_haploid_hi_error_no_variance/alignment/0.5X_haploid_hi_error_no_variance.sorted.bam outfile = results/0.5X_haploid_hi_error_no_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 = 8,036,521 (100%) number of supplementary alignments = 147 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,018,261 number of mapped paired reads (second in pair) = 4,018,260 number of mapped paired reads (both in pair) = 8,036,502 number of mapped paired reads (singletons) = 19 number of mapped bases = 1,201,706,510 bp number of sequenced bases = 1,201,695,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,564 duplication rate = 0.17% >>>>>>> Insert size mean insert size = 491.3727 std insert size = 73,406.0506 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 30.7853 >>>>>>> ACTG content number of A's = 352,756,645 bp (29.35%) number of C's = 253,253,880 bp (21.07%) number of T's = 347,604,298 bp (28.93%) number of G's = 248,078,732 bp (20.64%) number of N's = 2,054 bp (0%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.049 number of mismatches = 58,845,976 number of insertions = 7,145 mapped reads with insertion percentage = 0.09% number of deletions = 5,527 mapped reads with deletion percentage = 0.07% homopolymer indels = 25.37% >>>>>>> Coverage mean coverageData = 0.4984X std coverageData = 0.7176X There is a 38.74% 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 61194910 0.4988222698814632 0.7162377702413244 NC_006584.3 85426708 42717414 0.5000475261202855 0.7187370196342324 NC_006585.3 91889043 45836914 0.4988289408999504 0.7176686578439114 NC_006586.3 88276631 44043486 0.4989257689274526 0.7177825503889732 NC_006587.3 88915250 44328995 0.4985533415246541 0.7169338302405682 NC_006588.3 77573801 38669009 0.49848026655287914 0.7175052306558244 NC_006589.3 80974532 40385351 0.4987413943929926 0.7159524821604271 NC_006590.3 74330416 37071014 0.4987327664088413 0.717545515849526 NC_006591.3 61074082 30522810 0.4997669879016765 0.7194975993900423 NC_006592.3 69331447 34559993 0.4984749993751032 0.7170410900720952 NC_006593.3 74389097 37086557 0.49854828860202455 0.7158402788822708 NC_006594.3 72498081 36116664 0.4981740689108723 0.7157864121661449 NC_006595.3 63241923 31541540 0.49874416374087804 0.7152437370783391 NC_006596.3 60966679 30394269 0.49853902981987913 0.7180498516565651 NC_006597.3 64190966 31992259 0.4983919232497607 0.7159722016728346 NC_006598.3 59632846 29770081 0.49922287794213277 0.7164514660658743 NC_006599.3 64289059 32062444 0.49872318087592477 0.7159011183563291 NC_006600.3 55844845 27878631 0.4992158363050341 0.7184809354257069 NC_006601.3 53741614 26788743 0.49847298966495496 0.7162661808869154 NC_006602.3 58134056 28974492 0.49840823079676394 0.7176689569549018 NC_006603.3 50858623 25357889 0.4985956658716458 0.7182269009037915 NC_006604.3 61439934 30616927 0.4983229148651104 0.7168646202390084 NC_006605.3 52294480 26066765 0.49846111864961656 0.7177416922715999 NC_006606.3 47698779 23772993 0.49839835522833825 0.715454479605899 NC_006607.3 51628933 25737405 0.49850739700547364 0.7167344181356028 NC_006608.3 38964690 19417892 0.4983458613426669 0.7163753883841908 NC_006609.3 45876710 22865820 0.4984189145211154 0.7162357678491782 NC_006610.3 41182112 20532847 0.4985865465083481 0.7160329358998524 NC_006611.3 41845238 20852490 0.4983240864826722 0.7158087438631833 NC_006612.3 40214260 20040579 0.4983450895279436 0.7154292018198669 NC_006613.3 39895921 19875075 0.4981731089752258 0.716078014125032 NC_006614.3 38810281 19324551 0.4979235012495787 0.7174108811673097 NC_006615.3 31377067 15641286 0.4984942027882976 0.7131926056214183 NC_006616.3 42124431 20990081 0.49828758517830185 0.7148540887046126 NC_006617.3 26524999 13219025 0.49836099899570213 0.7153413187757415 NC_006618.3 30810995 15353842 0.4983234718645081 0.718060261246074 NC_006619.3 30902991 15409625 0.49864509878671615 0.7151115768202546 NC_006620.3 23914537 11924026 0.4986099459086329 0.7173372842469731 NC_006621.3 123869142 61721190 0.49827736757876306 0.717063685107367 NW_003726127.1 2660953 1334606 0.5015518876131972 0.7239273676582163 NW_003726128.1 1881673 938209 0.49860363623222526 0.7369971578166985 NW_003726129.1 1415205 716370 0.5061952155341453 0.7426720395653036 NW_003726130.1 1067467 538259 0.504239475318675 0.7429669237216383 NW_003726131.1 866315 435900 0.5031657076236704 0.7293441415863885 NW_003726132.1 881102 444821 0.504846203958225 0.7354457485892191 NW_003726133.1 822601 406080 0.4936536668445577 0.7231577682016814 NW_003726134.1 741967 372371 0.5018700292600614 0.7269148000844935 NW_003726135.1 745551 368988 0.49491986463702686 0.7445831520127261 NW_003726136.1 602611 304760 0.5057325538365546 0.7232074110118374 NW_003726137.1 573630 284491 0.4959486079877273 0.724429680712996 NW_003726138.1 666183 336755 0.5054992396984012 0.7485231966964856 NW_003726139.1 557017 278495 0.49997576375586383 0.7423709899235196 NW_003726140.1 510604 255567 0.5005189931923761 0.7181012520014642 NW_003726141.1 497093 246213 0.49530570738272317 0.7236748069053417 NW_003726142.1 492630 239123 0.4854008079085724 0.7259649591620443 NW_003726143.1 577062 283847 0.49188302123515326 0.7575065173765259 NW_003726144.1 561270 274583 0.48921731074171076 0.742939690336869 NW_003726145.1 407330 207173 0.5086121817690816 0.7252902381168916 NW_003726146.1 405216 201433 0.4971003119324015 0.7012411874381786 NW_003726147.1 508668 252164 0.495733956136419 0.7755540528853846 NW_003726148.1 540093 276558 0.5120562569779649 0.7872892147468096 NW_003726149.1 448434 224969 0.5016769468862754 0.7621883460828498 NW_003726150.1 377800 190206 0.5034568554790895 0.7255590679320575 NW_003726151.1 384880 191304 0.4970484306796924 0.7245950662607772 NW_003726152.1 367143 183057 0.4985986386775725 0.7339972816257055 NW_003726153.1 399987 202109 0.5052889218899614 0.7543590191726487 NW_003726154.1 376204 192591 0.5119323558494859 0.7446874848884109 NW_003726155.1 416178 210156 0.504966624857633 0.7541981778763264 NW_003726156.1 365470 185168 0.5066571811639806 0.7400923553263772 NW_003726157.1 322752 160899 0.49852208506841167 0.7207927687318978 NW_003726158.1 320591 162900 0.50812405837968 0.7276581967115175 NW_003726159.1 310270 155728 0.5019112385986398 0.7520931016308373 NW_003726160.1 433650 209669 0.4834982128444598 0.7818657632394251 NW_003726161.1 273228 133324 0.4879587743569473 0.7038521924763085 NW_003726162.1 281659 141797 0.503435004739774 0.756777295773866 NW_003726163.1 320442 159950 0.49915429313261056 0.7486248991265985 NW_003726164.1 265648 133916 0.5041107028850208 0.7311224999215051 NW_003726165.1 241365 118035 0.489031135417314 0.7176385695084387 NW_003726166.1 234529 119588 0.5099070903811469 0.7169716087409129 NW_003726167.1 252720 123863 0.49011949984172204 0.728336295309923 NW_003726168.1 254975 129095 0.5063045396607511 0.7366143548195551 NW_003726169.1 226053 109559 0.4846606769208991 0.6941871768848078 NW_003726170.1 223744 120296 0.537650171624714 0.75392550548997 NW_003726171.1 227140 114602 0.5045434533767721 0.73505272310921 NW_003726172.1 219672 109163 0.4969363414545322 0.7166792181362408 NW_003726173.1 214597 109525 0.510375261536741 0.7451546348598476 NW_003726174.1 386314 191610 0.4959954855376714 0.8423036166775101 NW_003726175.1 204342 103500 0.5065038024488357 0.7240732818317591 NW_003726176.1 201724 105385 0.5224217247328032 0.7404606447086647 NW_003726177.1 216332 109719 0.5071787807629015 0.7175733951033486 NW_003726178.1 200877 102398 0.5097547255285573 0.7403291938046778 NW_003726179.1 310654 147356 0.47434122850502486 0.7711784646005708 NW_003726180.1 200932 101288 0.504090936237135 0.728918586760038 NW_003726181.1 201410 101608 0.5044833920857952 0.7063250295724757 NW_003726182.1 292533 138987 0.475115627980433 0.7622479810243521 NW_003726183.1 192561 97998 0.5089192515618427 0.7256588936236937 NW_003726184.1 210134 107191 0.5101078359522971 0.7468450746550147 NW_003726185.1 197844 98555 0.4981450031337822 0.7422401905895807 NW_003726186.1 196813 100838 0.512354366835524 0.7244583281851319 NW_003726187.1 180359 87354 0.4843340226991722 0.6912544200683498 NW_003726188.1 210247 101546 0.48298429941925447 0.7705292820173125 NW_003726189.1 177735 91449 0.5145244324415562 0.7423862672512382 NW_003726190.1 172100 85510 0.4968622893666473 0.6994781222035179 NW_003726191.1 166866 84287 0.505117879016696 0.7054824733370605 NW_003726192.1 164926 86102 0.5220644410220341 0.7441415014739032 NW_003726193.1 157598 77513 0.4918399979695174 0.7231051380026103 NW_003726194.1 143980 71729 0.4981872482289207 0.7185191767908653 NW_003726195.1 141074 72089 0.51100131845698 0.7567148683373166 NW_003726196.1 139526 69917 0.5011037369379184 0.7043970027474907 NW_003726197.1 142260 73974 0.5199915647406158 0.7299608556692199 NW_003726198.1 138160 71807 0.5197379849449913 0.7438912313784232 NW_003726199.1 142296 74815 0.5257702254455501 0.7353328704508686 NW_003726200.1 133119 65504 0.49207100413915367 0.7148298820461721 NW_003726201.1 129748 64640 0.49819650399235443 0.7420000005709503 NW_003726202.1 125962 63326 0.5027389212619678 0.7089263790967444 NW_003726203.1 127429 63090 0.49509923172904124 0.7098962647907668 NW_003726204.1 128261 64786 0.5051106727688074 0.7297095083764152 NW_003726205.1 131872 66053 0.5008872239747634 0.7497972315218309 NW_003726206.1 133432 63155 0.4733122489357875 0.7527101519630675 NW_003726207.1 119670 58887 0.4920782150915016 0.7459424245047885 NW_003726208.1 144750 72659 0.5019620034542315 0.7437799310115905 NW_003726209.1 120779 60451 0.5005091944791727 0.7313347961068976 NW_003726210.1 115952 57997 0.5001811094245895 0.7235277789042565 NW_003726211.1 118237 58343 0.49344113940644635 0.7158773958813874 NW_003726212.1 111908 55099 0.4923597955463416 0.7198222553450684 NW_003726213.1 117332 65355 0.5570091705587563 0.7778718041283804 NW_003726214.1 111759 55710 0.49848334362333235 0.7165719513822361 NW_003726215.1 108801 55295 0.5082214317883108 0.7025060341910176 NW_003726216.1 112014 56879 0.5077847411930652 0.7623306347836818 NW_003726217.1 106428 52667 0.4948603750892622 0.6909513236006043 NW_003726218.1 104912 53751 0.5123436785115144 0.7157353549287783 NW_003726219.1 104646 49946 0.47728532385375455 0.6892208589533115 NW_003726220.1 103248 51310 0.4969587788625445 0.7418199310959943 NW_003726221.1 129482 61814 0.4773945413262075 0.7263588281746695 NW_003726222.1 118473 61325 0.5176284891916302 0.7782365953833855 NW_003726223.1 99993 46372 0.46375246267238707 0.7064302096204799 NW_003726224.1 109585 54095 0.49363507779349364 0.7411032475396466 NW_003726225.1 124049 58896 0.47478012720779694 0.7442478791001989 NW_003726226.1 99658 47826 0.47990126231712454 0.702274254907407 NW_003726227.1 101741 51073 0.5019903480406129 0.7300610445795547 NW_003726228.1 97365 48529 0.4984234581215016 0.7131703454350228 NW_003726229.1 94395 48405 0.5127919911012235 0.7261894131942633 NW_003726230.1 102992 49625 0.48183354046916266 0.7131366449843574 NW_003726231.1 95509 44844 0.46952643206399397 0.6776638476292166 NW_003726232.1 92047 45809 0.4976696687561789 0.7257716519623679 NW_003726233.1 87753 40663 0.46338016933894 0.6633344556709811 NW_003726234.1 96536 46358 0.4802146349548355 0.760742585800844 NW_003726235.1 86544 41899 0.48413523756701793 0.67315390615967 NW_003726236.1 85476 42148 0.4930974776545463 0.6848925964424584 NW_003726237.1 110512 56539 0.5116095989575793 0.7917423515576116 NW_003726238.1 83291 40364 0.4846141840054748 0.6752629375134578 NW_003726239.1 82459 41885 0.5079494051589275 0.7175271280803822 NW_003726240.1 81605 41276 0.5058023405428589 0.7106850570488429 NW_003726241.1 82380 42115 0.5112284535081331 0.703584048452988 NW_003726242.1 102198 48521 0.47477445742578134 0.731052490524095 NW_003726243.1 82108 39741 0.48400886637112095 0.6953835522336018 NW_003726244.1 87041 44266 0.50856492917131 0.7457855598016482 NW_003726245.1 79722 40422 0.5070369534131106 0.7064994124541001 NW_003726246.1 230124 111892 0.48622481792424954 0.9995204319141536 NW_003726247.1 78357 39147 0.4995979937976186 0.7145105889610674 NW_003726248.1 256406 123813 0.48287871578668207 1.0448256495988102 NW_003726249.1 78050 39714 0.5088276745675849 0.723455457688822 NW_003726250.1 81930 40997 0.5003905773221042 0.7199489341161394 NW_003726251.1 77100 39612 0.5137743190661479 0.7415623669686352 NW_003726252.1 77130 38743 0.502307792039414 0.7009845998031414 NW_003726253.1 79078 39410 0.4983686992589595 0.7355621656819549 NW_003726254.1 90550 45117 0.4982551076753175 0.8131119319515447 NW_003726255.1 82767 40980 0.4951248686070535 0.7112831023939032 NW_003726256.1 89070 43707 0.4907039407207814 0.7651453672753619 NW_003726257.1 97802 49089 0.50192225107871 0.7861596162312507 NW_003726258.1 79712 39795 0.49923474508229626 0.7038878080550445 NW_003726259.1 79581 41947 0.5270981767004687 0.7793370518964953 NW_003726260.1 73720 37677 0.5110824742268041 0.7404020114863857 NW_003726261.1 97799 45796 0.46826654669270645 0.7495999418894805 NW_003726262.1 73171 35921 0.4909185332987112 0.7047372717969943 NW_003726263.1 104732 53831 0.5139880838712142 0.7870167021565713 NW_003726264.1 78935 36791 0.46609235446886677 0.7112645140368341 NW_003726265.1 72992 36314 0.4975065760631302 0.7051039325827725 NW_003726266.1 68721 35614 0.5182404214141237 0.7460492474767461 NW_003726267.1 73611 37399 0.5080626536794772 0.7056688852097186 NW_003726268.1 68272 34136 0.5 0.7088239913179551 NW_003726269.1 79297 38219 0.48197283629897725 0.7063571626635262 NW_003726270.1 84443 42989 0.5090889712587189 0.7606352467152928 NW_003726271.1 80679 36206 0.44876609774538606 0.703931080495959 NW_003726272.1 68834 34652 0.5034140105180579 0.7224388653869478 NW_003726273.1 67496 33452 0.49561455493658885 0.6777581709311333 NW_003726274.1 66523 33231 0.49954151195827007 0.7341338316970863 NW_003726275.1 67057 33159 0.4944897624409085 0.7523887026129414 NW_003726276.1 66195 31329 0.47328348062542486 0.7117702169150013 NW_003726277.1 87584 43923 0.5014957069784436 0.795147384547623 NW_003726278.1 84679 35853 0.4233989536957215 0.6826459341455946 NW_003726279.1 65840 32551 0.4943955042527339 0.6838477988446321 NW_003726280.1 65696 34337 0.5226650024354603 0.7315304011645207 NW_003726281.1 66021 33503 0.5074597476560488 0.7745866581013652 NW_003726282.1 67300 31694 0.4709361069836553 0.7304474704328937 NW_003726283.1 88153 40323 0.4574206209658208 0.7221231687511643 NW_003726284.1 92437 39251 0.4246243387388167 0.7214764393528923 NW_003726285.1 70351 34295 0.48748418643658226 0.7310374218284519 NW_003726286.1 64646 34382 0.5318503851746434 0.7871787628092162 NW_003726287.1 69126 33916 0.4906402800682811 0.6915764519612226 NW_003726288.1 227674 97463 0.42808137951632597 0.9737021048694076 NW_003726289.1 64123 31070 0.4845375294356159 0.695587727653199 NW_003726290.1 61944 29931 0.48319449825648975 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0.630322476010543 NW_003729351.1 1790 894 0.4994413407821229 0.5977141940194164 NW_003729352.1 1685 897 0.5323442136498516 0.8882641493521967 NW_003729353.1 1573 292 0.1856325492689129 0.38880985831230863 NW_003729354.1 1115 900 0.8071748878923767 1.0363538191527646 NC_002008.4 16727 8356 0.4995516231242901 0.6503948719038168