BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_hi_error_med_variance/alignment/5X_hi_error_med_variance.sorted.bam outfile = results/5X_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 = 80,365,282 number of mapped reads = 80,364,555 (100%) number of supplementary alignments = 2,710 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,182,270 number of mapped paired reads (second in pair) = 40,182,285 number of mapped paired reads (both in pair) = 80,364,142 number of mapped paired reads (singletons) = 413 number of mapped bases = 11,996,955,251 bp number of sequenced bases = 11,988,993,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,367,770 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 572.0634 std insert size = 95,837.3152 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.221 >>>>>>> ACTG content number of A's = 3,515,097,034 bp (29.32%) number of C's = 2,530,527,252 bp (21.11%) number of T's = 3,463,957,535 bp (28.89%) number of G's = 2,479,392,725 bp (20.68%) number of N's = 19,221 bp (0%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0551 number of mismatches = 653,658,457 number of insertions = 5,533,086 mapped reads with insertion percentage = 6.67% number of deletions = 5,557,097 mapped reads with deletion percentage = 6.69% homopolymer indels = 27.62% >>>>>>> Coverage mean coverageData = 4.976X std coverageData = 2.3403X There is a 98.39% of reference with a coverageData >= 1X There is a 94.8% of reference with a coverageData >= 2X There is a 86.3% of reference with a coverageData >= 3X There is a 72.45% of reference with a coverageData >= 4X There is a 55.36% of reference with a coverageData >= 5X There is a 38.33% of reference with a coverageData >= 6X There is a 24.08% of reference with a coverageData >= 7X There is a 13.8% of reference with a coverageData >= 8X There is a 7.27% of reference with a coverageData >= 9X There is a 3.54% of reference with a coverageData >= 10X There is a 1.62% of reference with a coverageData >= 11X There is a 0.7% 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 0.03% 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 610816286 4.978988714307857 2.31212253661886 NC_006584.3 85426708 426332304 4.990620778691366 2.3161083462807297 NC_006585.3 91889043 457635913 4.980309926614428 2.3008772803521724 NC_006586.3 88276631 439581010 4.979585253995477 2.301291951778807 NC_006587.3 88915250 442541116 4.9771115303617774 2.300905599703747 NC_006588.3 77573801 386140476 4.977717618864648 2.31913250924382 NC_006589.3 80974532 403129183 4.978468822765163 2.3082352821131957 NC_006590.3 74330416 370099977 4.979118871068877 2.3066374478603495 NC_006591.3 61074082 304514043 4.985978225591667 2.3229688256383487 NC_006592.3 69331447 345069856 4.977104487664883 2.319241099646222 NC_006593.3 74389097 370329616 4.97827814740109 2.3026345900236658 NC_006594.3 72498081 360751829 4.976019006627224 2.296391207431544 NC_006595.3 63241923 314750400 4.976926460632767 2.3049303988909413 NC_006596.3 60966679 303527209 4.978575411660524 2.306025586137112 NC_006597.3 64190966 319376922 4.975418534751448 2.314267476266572 NC_006598.3 59632846 297197459 4.983787944650503 2.3233455210595833 NC_006599.3 64289059 320031213 4.978004313300028 2.2941111812164863 NC_006600.3 55844845 278056537 4.9790904961774 2.326835152418028 NC_006601.3 53741614 267446874 4.976532226962889 2.294827261257961 NC_006602.3 58134056 289254706 4.975649832518137 2.3149200650007358 NC_006603.3 50858623 253200228 4.9785112742828295 2.308472469550561 NC_006604.3 61439934 305655852 4.974872726914062 2.2965126610895052 NC_006605.3 52294480 260179589 4.9752782511653235 2.291890456360119 NC_006606.3 47698779 237408271 4.977240004403467 2.3045789019525316 NC_006607.3 51628933 256911943 4.976123426761502 2.3100917424166885 NC_006608.3 38964690 194057130 4.9803329629980375 2.3109397649190218 NC_006609.3 45876710 228243228 4.975143771207656 2.3093481337974975 NC_006610.3 41182112 204947236 4.976608193382603 2.3116842427669098 NC_006611.3 41845238 208136848 4.9739673603959424 2.3028402005774757 NC_006612.3 40214260 200100488 4.975859011206473 2.2955592648879666 NC_006613.3 39895921 198499921 4.975444005917296 2.296943128573869 NC_006614.3 38810281 193030165 4.973686353881334 2.283898204792105 NC_006615.3 31377067 156145442 4.976419306495409 2.3102839139821794 NC_006616.3 42124431 209532785 4.974139235257564 2.303432003394643 NC_006617.3 26524999 131942607 4.97427377848346 2.3026058450446825 NC_006618.3 30810995 153328371 4.976417379575051 2.299048647988611 NC_006619.3 30902991 153743373 4.9750321255311505 2.3025898433568965 NC_006620.3 23914537 119017840 4.976798839969178 2.3104790737579557 NC_006621.3 123869142 616466347 4.976754799835459 2.339123185049429 NW_003726127.1 2660953 13325853 5.007924980260832 2.515862621756535 NW_003726128.1 1881673 9383110 4.9865784331283916 2.851624662803658 NW_003726129.1 1415205 7065633 4.992656894230871 2.7555085114550844 NW_003726130.1 1067467 5330016 4.993143581956163 3.082871185638898 NW_003726131.1 866315 4326189 4.993782861892037 2.3104744607110255 NW_003726132.1 881102 4441117 5.040411893288177 2.7268727725420896 NW_003726133.1 822601 4121136 5.009884500505105 2.6580370522201475 NW_003726134.1 741967 3702308 4.989855343970824 2.281716521574883 NW_003726135.1 745551 3711552 4.978267080320461 3.330223990755752 NW_003726136.1 602611 3027117 5.023335120002788 2.466540163691822 NW_003726137.1 573630 2861063 4.987645346303366 2.403007071672488 NW_003726138.1 666183 3289271 4.937488648014134 3.1743975211211994 NW_003726139.1 557017 2783861 4.997802580531653 2.6319056762241586 NW_003726140.1 510604 2572496 5.0381430619423275 2.2877589181711184 NW_003726141.1 497093 2503031 5.035337451945612 2.422311331771825 NW_003726142.1 492630 2427320 4.927267929277551 2.516601283642138 NW_003726143.1 577062 2857092 4.951100574981544 3.4553414246473557 NW_003726144.1 561270 2759649 4.9167940563365224 3.4059258595933297 NW_003726145.1 407330 2038355 5.004185795301107 2.262429301263638 NW_003726146.1 405216 2031775 5.014054232804233 2.254450329232536 NW_003726147.1 508668 2519851 4.953822532575275 3.448415063853088 NW_003726148.1 540093 2680027 4.9621583690216315 4.025203013738387 NW_003726149.1 448434 2235864 4.985937729966952 3.3922845592609105 NW_003726150.1 377800 1887401 4.99576760190577 2.52026249814927 NW_003726151.1 384880 1922212 4.994315111203492 2.686621442517613 NW_003726152.1 367143 1837890 5.005924122208513 2.446231709390491 NW_003726153.1 399987 2015592 5.039143772172595 3.059175861731101 NW_003726154.1 376204 1863808 4.954248227025762 2.6992928805651615 NW_003726155.1 416178 2069191 4.971889431925763 3.3059166295105253 NW_003726156.1 365470 1826417 4.997447122882863 2.9692197634400443 NW_003726157.1 322752 1609002 4.985258030933968 2.343687441852629 NW_003726158.1 320591 1623405 5.063788440723538 2.3920230867281407 NW_003726159.1 310270 1544183 4.97690076385084 2.462181413737465 NW_003726160.1 433650 2124626 4.899402744148507 4.037682840607235 NW_003726161.1 273228 1383893 5.064975039161433 2.276939815814821 NW_003726162.1 281659 1414426 5.021767456392304 2.6010711086735303 NW_003726163.1 320442 1604464 5.007034034240205 3.252256869307473 NW_003726164.1 265648 1332127 5.01463214479311 2.3365622094099048 NW_003726165.1 241365 1241466 5.143521223043938 2.4303842499369654 NW_003726166.1 234529 1181971 5.039764805205326 2.3591932241826 NW_003726167.1 252720 1297575 5.134437321937322 2.955099846265853 NW_003726168.1 254975 1282020 5.0280223551328564 3.0396892455264393 NW_003726169.1 226053 1135883 5.024852578820012 2.3945222709005423 NW_003726170.1 223744 1135532 5.075139445080092 2.4493692327085204 NW_003726171.1 227140 1141831 5.026992163423439 2.5061632066981883 NW_003726172.1 219672 1089326 4.958875050074656 2.3102009740312104 NW_003726173.1 214597 1070870 4.990144317022139 2.293566131956336 NW_003726174.1 386314 1916638 4.96134750487945 5.167566487848371 NW_003726175.1 204342 1017196 4.977909582954068 2.36640446091207 NW_003726176.1 201724 1020210 5.057454740139994 2.372251125564694 NW_003726177.1 216332 1086976 5.024573340975907 2.7079365057534757 NW_003726178.1 200877 998121 4.968816738601234 2.2965497389651324 NW_003726179.1 310654 1490505 4.797958500453881 4.283071822477435 NW_003726180.1 200932 1002531 4.989404375609659 2.5143515733091886 NW_003726181.1 201410 1006969 4.999597835261407 2.381830551052317 NW_003726182.1 292533 1411836 4.826245244126303 4.0921690016338435 NW_003726183.1 192561 966688 5.020165038611141 2.2803828661211685 NW_003726184.1 210134 1066379 5.074757059780902 2.8300596920554644 NW_003726185.1 197844 1002232 5.065768989709063 2.721325924577762 NW_003726186.1 196813 1002972 5.096065808661013 2.8651859317977872 NW_003726187.1 180359 897063 4.973763438475485 2.2302672607103 NW_003726188.1 210247 994574 4.730502694449862 3.1534933811032517 NW_003726189.1 177735 919069 5.171007398655301 2.5139436812746196 NW_003726190.1 172100 868747 5.047919814061592 2.3355459206423337 NW_003726191.1 166866 852894 5.11125094387113 2.4475521219489087 NW_003726192.1 164926 839872 5.092417205292071 2.460577588454435 NW_003726193.1 157598 792627 5.029422962220333 2.8186913459820238 NW_003726194.1 143980 716292 4.974940964022781 2.4752326978646764 NW_003726195.1 141074 706849 5.0104838595347125 2.2179627022980113 NW_003726196.1 139526 693967 4.973746828548085 2.289250647732467 NW_003726197.1 142260 711702 5.0028258118937154 2.576687632274837 NW_003726198.1 138160 695636 5.035002895193978 2.2890192843627735 NW_003726199.1 142296 710447 4.992740484623601 2.4947000246891093 NW_003726200.1 133119 663140 4.981557854250708 2.2855586463871473 NW_003726201.1 129748 647725 4.99217714338564 2.2209715889727963 NW_003726202.1 125962 653620 5.189025261586828 2.3665080895473523 NW_003726203.1 127429 633519 4.971544938750206 2.3623533821651685 NW_003726204.1 128261 637858 4.973125112076157 2.442565874269521 NW_003726205.1 131872 653579 4.956162035913613 2.755687874164968 NW_003726206.1 133432 666003 4.991328916601715 2.8309166861351422 NW_003726207.1 119670 601485 5.026197041865129 2.2354336321970325 NW_003726208.1 144750 689365 4.762452504317789 3.3311940791789905 NW_003726209.1 120779 603840 4.999544622823504 2.515424981253604 NW_003726210.1 115952 580276 5.004450117289913 2.2316268897777105 NW_003726211.1 118237 577776 4.88659218349586 2.5758255292981787 NW_003726212.1 111908 549284 4.908353290202666 2.363984937600022 NW_003726213.1 117332 603777 5.145885180513415 2.7752301856397077 NW_003726214.1 111759 556559 4.97999266278331 2.364344362899245 NW_003726215.1 108801 555861 5.108969586676593 2.4061697873345853 NW_003726216.1 112014 569621 5.085266127448355 2.6660906896931595 NW_003726217.1 106428 544515 5.11627579208479 2.374639121374162 NW_003726218.1 104912 529486 5.046953637334147 2.3941353442471254 NW_003726219.1 104646 520134 4.970414540450662 2.177239310384733 NW_003726220.1 103248 515299 4.990886022005268 2.3793017971984494 NW_003726221.1 129482 628823 4.856451089726757 3.585718518740328 NW_003726222.1 118473 589279 4.973951870890414 3.168426469548462 NW_003726223.1 99993 507857 5.078925524786735 2.2800584495449243 NW_003726224.1 109585 532507 4.859305561892595 2.811780746706923 NW_003726225.1 124049 596309 4.807043990681102 3.2875011186427665 NW_003726226.1 99658 492498 4.941881233819664 2.4360816039046225 NW_003726227.1 101741 505973 4.973147501990348 2.6948183607624734 NW_003726228.1 97365 488660 5.018846608124069 2.3285253226775446 NW_003726229.1 94395 478920 5.0735738121722544 2.4460673225158787 NW_003726230.1 102992 470242 4.565810936771788 2.8546667391012055 NW_003726231.1 95509 462145 4.838758651017182 2.5305150289782206 NW_003726232.1 92047 467282 5.076558714569731 2.417399979960904 NW_003726233.1 87753 449246 5.119437512107848 2.409205251340445 NW_003726234.1 96536 461402 4.7795848180989475 3.1054187920494956 NW_003726235.1 86544 440147 5.085817618783509 2.319578318097561 NW_003726236.1 85476 425410 4.9769525948804345 2.229339916462854 NW_003726237.1 110512 534906 4.840252642246996 3.7078535632029257 NW_003726238.1 83291 414174 4.972614087956682 2.2678655668576497 NW_003726239.1 82459 424939 5.153336809808511 2.322347166803696 NW_003726240.1 81605 420662 5.154855707370872 2.4153987562556747 NW_003726241.1 82380 425607 5.166387472687545 2.606886662949051 NW_003726242.1 102198 485360 4.749212313352512 3.6709371750013053 NW_003726243.1 82108 406728 4.953573342427047 2.397958391758547 NW_003726244.1 87041 439320 5.047276570811457 2.8683767490057046 NW_003726245.1 79722 406476 5.098667870851208 2.2343307875885614 NW_003726246.1 230124 1123982 4.88424501573065 7.2985490524235805 NW_003726247.1 78357 387959 4.951172199037738 2.3693972134418644 NW_003726248.1 256406 1254358 4.8920774084849805 7.889880469147178 NW_003726249.1 78050 394814 5.05847533632287 2.352086321173543 NW_003726250.1 81930 411877 5.0271817405101915 2.6812330230777954 NW_003726251.1 77100 384835 4.991374837872892 2.3327614192157538 NW_003726252.1 77130 384097 4.979865162712304 2.371334425832896 NW_003726253.1 79078 398456 5.038771845519614 2.5652653112989303 NW_003726254.1 90550 435361 4.807962451684152 3.31158065186241 NW_003726255.1 82767 421576 5.09352761366245 3.0644907284620215 NW_003726256.1 89070 402268 4.516313012237566 3.1082261678610035 NW_003726257.1 97802 484214 4.950962148013333 3.6094077523796533 NW_003726258.1 79712 396795 4.977857788036933 2.889930941446849 NW_003726259.1 79581 408921 5.138425000942436 2.8732785411049004 NW_003726260.1 73720 368248 4.995225176342919 2.330150130126467 NW_003726261.1 97799 481422 4.9225656704056275 3.781788900345842 NW_003726262.1 73171 368457 5.035560536278034 2.211185405972125 NW_003726263.1 104732 513703 4.904928770576328 4.002157611717287 NW_003726264.1 78935 389797 4.93820231836321 2.860010064129464 NW_003726265.1 72992 375556 5.145166593599298 2.424462174138399 NW_003726266.1 68721 349254 5.0822019470030995 2.305559308037731 NW_003726267.1 73611 355994 4.8361522055127635 2.614109520032976 NW_003726268.1 68272 340262 4.983917272088118 2.270646689420601 NW_003726269.1 79297 393781 4.9659003493196465 3.290095863027934 NW_003726270.1 84443 412196 4.881351917861753 3.491363909478901 NW_003726271.1 80679 382288 4.738382974503899 3.244646292648802 NW_003726272.1 68834 341636 4.963186797222303 2.4656134943635637 NW_003726273.1 67496 335620 4.9724428114258625 2.439611193033261 NW_003726274.1 66523 330810 4.972866527366475 2.306826204753028 NW_003726275.1 67057 332283 4.955232115961048 2.311876423086298 NW_003726276.1 66195 329598 4.979197824609109 2.334701158112112 NW_003726277.1 87584 400552 4.573346729996346 3.5945654275737677 NW_003726278.1 84679 387788 4.5795061349331005 3.3879624275688838 NW_003726279.1 65840 330485 5.019517010935601 2.33720265354155 NW_003726280.1 65696 328445 4.999467243058938 2.284793706986654 NW_003726281.1 66021 330798 5.010496660153588 2.371685904655583 NW_003726282.1 67300 339289 5.041441307578009 2.5382629484694474 NW_003726283.1 88153 409941 4.650335212641657 3.8418983523539256 NW_003726284.1 92437 435318 4.70934798835964 4.001775841252019 NW_003726285.1 70351 343215 4.878608690708021 2.9819647386449755 NW_003726286.1 64646 328937 5.0882807907681835 2.563443691163947 NW_003726287.1 69126 340600 4.92723432572404 2.8575150390543937 NW_003726288.1 227674 1001745 4.399909519751926 7.62039175918266 NW_003726289.1 64123 318267 4.963382873539915 2.4422925062698138 NW_003726290.1 61944 300533 4.851688621981144 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