BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_haploid_hi_error_low_variance/alignment/5X_haploid_hi_error_low_variance.sorted.bam outfile = results/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 = 80,365,282 number of mapped reads = 80,365,056 (100%) number of supplementary alignments = 1,715 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,182,525 number of mapped paired reads (second in pair) = 40,182,531 number of mapped paired reads (both in pair) = 80,364,912 number of mapped paired reads (singletons) = 144 number of mapped bases = 12,014,497,879 bp number of sequenced bases = 12,013,200,941 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,350,720 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 501.1931 std insert size = 81,627.0491 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.4723 >>>>>>> ACTG content number of A's = 3,525,500,058 bp (29.35%) number of C's = 2,532,659,458 bp (21.08%) number of T's = 3,474,114,095 bp (28.92%) number of G's = 2,480,907,566 bp (20.65%) number of N's = 19,764 bp (0%) GC percentage = 41.73% >>>>>>> Mismatches and indels general error rate = 0.0499 number of mismatches = 598,317,635 number of insertions = 896,679 mapped reads with insertion percentage = 1.11% number of deletions = 890,697 mapped reads with deletion percentage = 1.1% homopolymer indels = 27.45% >>>>>>> Coverage mean coverageData = 4.9832X std coverageData = 2.3411X There is a 98.41% of reference with a coverageData >= 1X There is a 94.87% of reference with a coverageData >= 2X There is a 86.41% of reference with a coverageData >= 3X There is a 72.61% of reference with a coverageData >= 4X There is a 55.52% of reference with a coverageData >= 5X There is a 38.48% of reference with a coverageData >= 6X There is a 24.2% of reference with a coverageData >= 7X There is a 13.88% of reference with a coverageData >= 8X There is a 7.32% of reference with a coverageData >= 9X There is a 3.57% of reference with a coverageData >= 10X There is a 1.63% of reference with a coverageData >= 11X There is a 0.71% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 611765564 4.986726629221181 2.3139617748988486 NC_006584.3 85426708 426852339 4.996708277696947 2.3189825826474837 NC_006585.3 91889043 458338772 4.98795892345946 2.3071013119996198 NC_006586.3 88276631 440241295 4.987064979858599 2.3013674973343337 NC_006587.3 88915250 443175903 4.984250766881947 2.2994087900084064 NC_006588.3 77573801 386697075 4.984892708815441 2.3179682056996063 NC_006589.3 80974532 403708725 4.985625912601755 2.3098422159950682 NC_006590.3 74330416 370642944 4.986423646545985 2.307681506805584 NC_006591.3 61074082 305021454 4.994286348831244 2.326839315745666 NC_006592.3 69331447 345609489 4.984887867694439 2.3169840401084385 NC_006593.3 74389097 370882694 4.985713081044659 2.3034598640955144 NC_006594.3 72498081 361250617 4.982899023216905 2.2993541530135886 NC_006595.3 63241923 315231911 4.984540255045692 2.307212564465822 NC_006596.3 60966679 303926070 4.985117690271435 2.301985014129231 NC_006597.3 64190966 319836450 4.982577299117137 2.3081917555694287 NC_006598.3 59632846 297681147 4.9918990450330005 2.318501937054264 NC_006599.3 64289059 320494599 4.985212164950182 2.2958867672293164 NC_006600.3 55844845 278438476 4.985929784566507 2.3222112274948956 NC_006601.3 53741614 267856228 4.984149303740673 2.2963172139294303 NC_006602.3 58134056 289675057 4.98288055111792 2.3145304661564734 NC_006603.3 50858623 253531562 4.985026079058413 2.315096421344272 NC_006604.3 61439934 306086178 4.981876738344153 2.2993346272776267 NC_006605.3 52294480 260529266 4.981964941615253 2.2930778024222853 NC_006606.3 47698779 237734291 4.984074980200227 2.3083226732459083 NC_006607.3 51628933 257222544 4.982139452697967 2.315221520087067 NC_006608.3 38964690 194368122 4.988314343062911 2.313953118873452 NC_006609.3 45876710 228597767 4.982871853714009 2.302894470259813 NC_006610.3 41182112 205250967 4.983983507208178 2.3083884855956915 NC_006611.3 41845238 208418702 4.980702989429765 2.3060121994822063 NC_006612.3 40214260 200359538 4.982300756000483 2.2967805121437683 NC_006613.3 39895921 198784569 4.982578770396102 2.294554195935377 NC_006614.3 38810281 193350815 4.981948339925702 2.2888716232978923 NC_006615.3 31377067 156369599 4.983563282062023 2.3006055663920795 NC_006616.3 42124431 209842881 4.981500664068317 2.3005033585742805 NC_006617.3 26524999 132139544 4.981698359347723 2.299829697774907 NC_006618.3 30810995 153524355 4.982778225759993 2.2992821282383487 NC_006619.3 30902991 153957327 4.981955533042093 2.3096057851533254 NC_006620.3 23914537 119192055 4.984083739526297 2.3188664134195784 NC_006621.3 123869142 617354404 4.983924115660702 2.337343119548255 NW_003726127.1 2660953 13347819 5.016179917495724 2.5079319741275388 NW_003726128.1 1881673 9381170 4.985547435712794 2.89309803583406 NW_003726129.1 1415205 7035142 4.971111605739098 2.76936772814712 NW_003726130.1 1067467 5339487 5.002015987379469 3.0661504181431933 NW_003726131.1 866315 4328232 4.996141126495559 2.3111751182867635 NW_003726132.1 881102 4456255 5.057592651021108 2.744500677046836 NW_003726133.1 822601 4136334 5.0283600433259865 2.642698493197703 NW_003726134.1 741967 3715628 5.0078076248674135 2.293605784847804 NW_003726135.1 745551 3714300 4.981952944868962 3.30989303287432 NW_003726136.1 602611 3020303 5.012027659634491 2.4582923432166277 NW_003726137.1 573630 2860643 4.98691316702404 2.433158652560366 NW_003726138.1 666183 3312009 4.971620410607896 3.1685797219198153 NW_003726139.1 557017 2799521 5.025916623729617 2.6096048406814205 NW_003726140.1 510604 2561032 5.0156912205936495 2.2730495276997997 NW_003726141.1 497093 2486758 5.0026011229287075 2.487784279512939 NW_003726142.1 492630 2456146 4.985782433063354 2.566652025511374 NW_003726143.1 577062 2869553 4.9726944418450705 3.4853724266553163 NW_003726144.1 561270 2758793 4.9152689436456605 3.3921601996462707 NW_003726145.1 407330 2042997 5.015581960572509 2.3374056650358876 NW_003726146.1 405216 2034688 5.021242991392245 2.2560358794299127 NW_003726147.1 508668 2525937 4.965787114581613 3.4620013839031127 NW_003726148.1 540093 2700275 4.999648208734421 4.05672628527993 NW_003726149.1 448434 2227132 4.966465522239616 3.351465206525582 NW_003726150.1 377800 1891267 5.006000529380625 2.4861036040816233 NW_003726151.1 384880 1924823 5.001099043857826 2.6987452990205836 NW_003726152.1 367143 1834653 4.997107394121636 2.4773399526446513 NW_003726153.1 399987 2002946 5.007527744651701 2.980542044026743 NW_003726154.1 376204 1882853 5.004872356487438 2.709701824579548 NW_003726155.1 416178 2064386 4.960343891315735 3.278861837319814 NW_003726156.1 365470 1833393 5.016534872903384 3.040501489934129 NW_003726157.1 322752 1630610 5.052207267499504 2.412661106144951 NW_003726158.1 320591 1620212 5.053828710101032 2.4278366206794737 NW_003726159.1 310270 1549680 4.9946175911303055 2.404367725601796 NW_003726160.1 433650 2123262 4.896257350397787 4.007308081151282 NW_003726161.1 273228 1364452 4.993822009457303 2.3490983202095976 NW_003726162.1 281659 1406980 4.995331233867904 2.5326139951480253 NW_003726163.1 320442 1617064 5.046354722539492 3.31823343311715 NW_003726164.1 265648 1335831 5.028575408058784 2.329200481130326 NW_003726165.1 241365 1225664 5.0780519130777035 2.2778816315960326 NW_003726166.1 234529 1182261 5.041001326062022 2.316039913188084 NW_003726167.1 252720 1275085 5.045445552389997 2.9449147374535687 NW_003726168.1 254975 1283878 5.0353093440533385 3.0261309745672853 NW_003726169.1 226053 1133201 5.01298810455955 2.3954586780287253 NW_003726170.1 223744 1139584 5.09324942791762 2.5223718991306865 NW_003726171.1 227140 1129514 4.972765695165977 2.416030998849085 NW_003726172.1 219672 1093537 4.978044539131068 2.350060740134915 NW_003726173.1 214597 1087997 5.069954379604561 2.334952644479863 NW_003726174.1 386314 1918457 4.9660561097966935 5.1844625534734865 NW_003726175.1 204342 1016190 4.972986463869395 2.2641145272943715 NW_003726176.1 201724 1017081 5.041943447482699 2.3122813335266446 NW_003726177.1 216332 1071558 4.953303256106355 2.6983677304740197 NW_003726178.1 200877 999808 4.977214912608213 2.209216355824481 NW_003726179.1 310654 1490392 4.7975947517173445 4.26107215203142 NW_003726180.1 200932 995629 4.955054446280333 2.4358377852207473 NW_003726181.1 201410 1006275 4.996152127501117 2.4781396534926357 NW_003726182.1 292533 1407419 4.811146092919431 4.100705327353652 NW_003726183.1 192561 969465 5.034586442737626 2.318964817998298 NW_003726184.1 210134 1093293 5.202837237191506 2.8730261327645343 NW_003726185.1 197844 1000839 5.058728088797234 2.8266577535475466 NW_003726186.1 196813 1026898 5.217632981561177 2.8430138095617754 NW_003726187.1 180359 904936 5.017415266219041 2.237527385262275 NW_003726188.1 210247 1002787 4.769566272051445 3.2589011877966896 NW_003726189.1 177735 910134 5.120735927082454 2.428830664710104 NW_003726190.1 172100 876939 5.0955200464846016 2.352802605938409 NW_003726191.1 166866 843981 5.057836827154723 2.281898237218993 NW_003726192.1 164926 843261 5.112965814971563 2.3651906854627476 NW_003726193.1 157598 792631 5.029448343253087 2.745414619163065 NW_003726194.1 143980 717991 4.986741214057508 2.4953240599797315 NW_003726195.1 141074 700535 4.965727206997746 2.395991100266843 NW_003726196.1 139526 703847 5.044558003526224 2.2756722535206095 NW_003726197.1 142260 737187 5.181969633066217 2.6156077377667195 NW_003726198.1 138160 709104 5.132484076433121 2.326791449476346 NW_003726199.1 142296 715768 5.030134367796705 2.589320852651187 NW_003726200.1 133119 665549 4.999654444519566 2.3060921407500654 NW_003726201.1 129748 652438 5.028501402719117 2.140410829330507 NW_003726202.1 125962 648427 5.147798542417554 2.4020866747096368 NW_003726203.1 127429 636487 4.994836340236524 2.349034190065 NW_003726204.1 128261 643420 5.016489813739173 2.481929295771506 NW_003726205.1 131872 659619 5.001964025721912 2.74061377301508 NW_003726206.1 133432 679962 5.0959440014389354 2.7438809108866837 NW_003726207.1 119670 599539 5.009935656388402 2.3331934284964815 NW_003726208.1 144750 685158 4.733388601036269 3.2630128078968537 NW_003726209.1 120779 607866 5.032878232143005 2.562263692561065 NW_003726210.1 115952 579985 5.001940458120601 2.307118609142337 NW_003726211.1 118237 573605 4.851315578033949 2.4238939993859834 NW_003726212.1 111908 559810 5.002412696143261 2.3435890459975344 NW_003726213.1 117332 610034 5.199212491051035 2.7831202523834193 NW_003726214.1 111759 557052 4.984403940622232 2.4705408865263894 NW_003726215.1 108801 559257 5.140182535086994 2.470990843016448 NW_003726216.1 112014 576204 5.144035566982699 2.6303324344134116 NW_003726217.1 106428 535147 5.028253842973654 2.3573558077097694 NW_003726218.1 104912 539551 5.142891184993137 2.340146760011545 NW_003726219.1 104646 526137 5.027779370448942 2.3093380216104937 NW_003726220.1 103248 515449 4.99233883465055 2.399868500312492 NW_003726221.1 129482 632201 4.882539658021964 3.591812457536775 NW_003726222.1 118473 585617 4.943041874519933 3.157502242059286 NW_003726223.1 99993 507387 5.074225195763703 2.2990437021450383 NW_003726224.1 109585 540880 4.935712004380162 2.7154624197785955 NW_003726225.1 124049 588060 4.740546074535063 3.2820144294803226 NW_003726226.1 99658 492097 4.937857472556142 2.3749239962139415 NW_003726227.1 101741 506459 4.977924337287819 2.7027703578839826 NW_003726228.1 97365 485819 4.989667745082936 2.409001220581017 NW_003726229.1 94395 475607 5.038476614227449 2.4142170040437834 NW_003726230.1 102992 501815 4.872368727668168 2.922424285347716 NW_003726231.1 95509 464922 4.867834444921421 2.598938224092899 NW_003726232.1 92047 459346 4.990341890555912 2.480105767663499 NW_003726233.1 87753 434637 4.952958873200916 2.3596170613542835 NW_003726234.1 96536 462925 4.795361315985747 3.0383294576465953 NW_003726235.1 86544 432801 5.000935940099834 2.3592864061349763 NW_003726236.1 85476 421801 4.934730216669006 2.1691307789474057 NW_003726237.1 110512 548802 4.96599464311568 3.852764289266364 NW_003726238.1 83291 416623 5.002017024648522 2.255569750800459 NW_003726239.1 82459 430607 5.222074000412326 2.324550330417876 NW_003726240.1 81605 424810 5.205685926107469 2.6556551511323185 NW_003726241.1 82380 424467 5.152549162418063 2.550979633644477 NW_003726242.1 102198 493123 4.8251727039668095 3.6916239522395853 NW_003726243.1 82108 412076 5.018707068738735 2.454442712826044 NW_003726244.1 87041 435242 5.000425087027953 2.98660284267494 NW_003726245.1 79722 405630 5.088055994581169 2.2555822097325366 NW_003726246.1 230124 1126239 4.8940527715492514 7.31322623214162 NW_003726247.1 78357 389617 4.972331763594829 2.16825987227399 NW_003726248.1 256406 1253049 4.886972223738914 7.903531359848586 NW_003726249.1 78050 399878 5.123356822549647 2.280057302415726 NW_003726250.1 81930 407958 4.979348224093738 2.674915206807524 NW_003726251.1 77100 383429 4.973138780804151 2.3509182019745722 NW_003726252.1 77130 383108 4.967042655257358 2.3372495747266653 NW_003726253.1 79078 391957 4.956587167100837 2.6057975545692154 NW_003726254.1 90550 447207 4.938785201546107 3.425760189242491 NW_003726255.1 82767 420114 5.0758635688136575 3.0675339823467853 NW_003726256.1 89070 426650 4.790052767486247 3.318676871771466 NW_003726257.1 97802 490607 5.016328909429255 3.702400146329612 NW_003726258.1 79712 397203 4.982976214371738 2.6277175878077226 NW_003726259.1 79581 406675 5.1102021839383776 2.852918815571075 NW_003726260.1 73720 373943 5.072476939772111 2.3014526124426955 NW_003726261.1 97799 477561 4.883086739128212 3.8324523354944238 NW_003726262.1 73171 369186 5.045523499747167 2.270831150451538 NW_003726263.1 104732 517248 4.938777069090631 3.9769935923574504 NW_003726264.1 78935 376339 4.767707607525179 2.717526934429475 NW_003726265.1 72992 371695 5.092270385795704 2.576884846128606 NW_003726266.1 68721 349363 5.083788070604328 2.314239086693202 NW_003726267.1 73611 356695 4.845675238755077 2.8363383516160754 NW_003726268.1 68272 340590 4.9887215842512305 2.258660695834468 NW_003726269.1 79297 388915 4.904536111076081 3.183062867982795 NW_003726270.1 84443 418544 4.956526887959925 3.507826017757453 NW_003726271.1 80679 374107 4.636981122720906 3.1029823004875214 NW_003726272.1 68834 344474 5.004416422116977 2.4664555931630185 NW_003726273.1 67496 335893 4.9764874955552925 2.4209234630367673 NW_003726274.1 66523 336913 5.064609232896893 2.320296013160412 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