BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_low_error_low_variance/alignment/5X_low_error_low_variance.sorted.bam outfile = results/5X_low_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 = 80,365,282 (100%) number of supplementary alignments = 3 (0%) 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 = 12,054,655,370 bp number of sequenced bases = 12,053,844,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,340,757 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 354.2441 std insert size = 12,552.6324 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 32.349 >>>>>>> ACTG content number of A's = 3,537,629,995 bp (29.35%) number of C's = 2,490,293,773 bp (20.66%) number of T's = 3,536,918,635 bp (29.34%) number of G's = 2,488,980,861 bp (20.65%) number of N's = 21,221 bp (0%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 19,700,122 number of insertions = 567,935 mapped reads with insertion percentage = 0.7% number of deletions = 571,794 mapped reads with deletion percentage = 0.71% homopolymer indels = 28.89% >>>>>>> Coverage mean coverageData = 4.9999X std coverageData = 2.3301X There is a 98.45% of reference with a coverageData >= 1X There is a 94.98% of reference with a coverageData >= 2X There is a 86.63% of reference with a coverageData >= 3X There is a 72.92% of reference with a coverageData >= 4X There is a 55.88% of reference with a coverageData >= 5X There is a 38.8% 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 7.4% 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 613820363 5.0034760533371765 2.3073139965061364 NC_006584.3 85426708 428403025 5.014860516455814 2.3161182854047238 NC_006585.3 91889043 459782260 5.003667956363415 2.298514593225436 NC_006586.3 88276631 441738345 5.004023601670979 2.2932308014172507 NC_006587.3 88915250 444728472 5.001711989788029 2.2974441204553075 NC_006588.3 77573801 388031904 5.002099922885047 2.317556580877719 NC_006589.3 80974532 404925921 5.000657750019475 2.3020647495243036 NC_006590.3 74330416 371720603 5.000921870261025 2.295606401095775 NC_006591.3 61074082 305879245 5.008331439185611 2.3163706564345308 NC_006592.3 69331447 346617628 4.999428729649909 2.31215897201637 NC_006593.3 74389097 372049971 5.001404587556696 2.2915330421529463 NC_006594.3 72498081 362430044 4.999167412445027 2.28727105377714 NC_006595.3 63241923 316209683 5.0000010752361215 2.2991315773001593 NC_006596.3 60966679 304907040 5.001207954922393 2.2930300258647107 NC_006597.3 64190966 320947257 4.999882023897257 2.3051689878092376 NC_006598.3 59632846 298667573 5.008440700616569 2.3191440831617283 NC_006599.3 64289059 321631272 5.002892825045083 2.2928497878139544 NC_006600.3 55844845 279331925 5.001928557595603 2.3099154638818873 NC_006601.3 53741614 268717617 5.0001776463207825 2.28836096079901 NC_006602.3 58134056 290673273 5.00005148445173 2.305743053592736 NC_006603.3 50858623 254321535 5.000558803961327 2.3004632205445383 NC_006604.3 61439934 307194262 4.999911979072113 2.2827412388535238 NC_006605.3 52294480 261385676 4.998341622289772 2.28551791523882 NC_006606.3 47698779 238573741 5.001673963184676 2.304681922629251 NC_006607.3 51628933 258089275 4.998927151951794 2.3036053755138983 NC_006608.3 38964690 195033523 5.00539136844153 2.3067246922153117 NC_006609.3 45876710 229353411 4.999343043561755 2.2916839372889513 NC_006610.3 41182112 205906786 4.999908358269726 2.306299429059844 NC_006611.3 41845238 209197276 4.999309025318484 2.2897973798518603 NC_006612.3 40214260 201035906 4.999119864446095 2.29504450023413 NC_006613.3 39895921 199483959 5.0001091339638455 2.291937258893316 NC_006614.3 38810281 194022321 4.999250610939921 2.282948472216751 NC_006615.3 31377067 156946618 5.001953114355781 2.2933186327291 NC_006616.3 42124431 210574128 4.998859877774966 2.2949423712723624 NC_006617.3 26524999 132631061 5.000228689923796 2.294308624205509 NC_006618.3 30810995 154040261 4.999522443205745 2.295268945036867 NC_006619.3 30902991 154499939 4.999514092341418 2.3140816707856033 NC_006620.3 23914537 119592248 5.00081803799923 2.313087382317078 NC_006621.3 123869142 619250466 4.999231091792014 2.3085551527775934 NW_003726127.1 2660953 13345293 5.015230633536181 2.4294738037754144 NW_003726128.1 1881673 9442118 5.0179377607055 2.8727314618983906 NW_003726129.1 1415205 7108697 5.02308640797623 2.709507161907272 NW_003726130.1 1067467 5357881 5.019247433410119 3.0728792332343997 NW_003726131.1 866315 4345403 5.015961861447626 2.2961742232964433 NW_003726132.1 881102 4432949 5.031141683936706 2.691874747555062 NW_003726133.1 822601 4150218 5.045238213909295 2.605442718425934 NW_003726134.1 741967 3720335 5.014151572778843 2.3150689917437566 NW_003726135.1 745551 3730686 5.003931320593762 3.2659070108423927 NW_003726136.1 602611 3016065 5.004994930394567 2.336316512074715 NW_003726137.1 573630 2872856 5.008203894496452 2.397124421110244 NW_003726138.1 666183 3326936 4.994027166709448 3.163213243430724 NW_003726139.1 557017 2812974 5.050068489830651 2.686308221761474 NW_003726140.1 510604 2578722 5.0503364642658495 2.3118803685936116 NW_003726141.1 497093 2484251 4.997557801055335 2.386411626390532 NW_003726142.1 492630 2465611 5.004995635669772 2.584604948942311 NW_003726143.1 577062 2876317 4.984415885987987 3.517179347076887 NW_003726144.1 561270 2789407 4.969813102428422 3.3945975709865115 NW_003726145.1 407330 2052280 5.038371836103405 2.3253470071607696 NW_003726146.1 405216 2056296 5.074567638000474 2.316158974816202 NW_003726147.1 508668 2536200 4.985963339545637 3.4812503961521517 NW_003726148.1 540093 2689153 4.9790554589672515 4.03376563171455 NW_003726149.1 448434 2225572 4.962986749443619 3.239255010794993 NW_003726150.1 377800 1900805 5.031246691371096 2.473350252785045 NW_003726151.1 384880 1921774 4.993177094159218 2.6921386646074925 NW_003726152.1 367143 1831234 4.987794946383289 2.413237513935035 NW_003726153.1 399987 2002072 5.005342673636894 2.995185764300156 NW_003726154.1 376204 1879760 4.996650753314691 2.696901827546732 NW_003726155.1 416178 2071791 4.9781367587907095 3.2617218743164753 NW_003726156.1 365470 1829945 5.00710044600104 2.946102805171359 NW_003726157.1 322752 1629860 5.0498835018838 2.331426475860204 NW_003726158.1 320591 1636508 5.104659831373931 2.443411761550349 NW_003726159.1 310270 1550995 4.998855835240275 2.487986581465831 NW_003726160.1 433650 2151357 4.961044621238326 4.057029040820877 NW_003726161.1 273228 1367072 5.003411070607697 2.3094243792644176 NW_003726162.1 281659 1411997 5.013143553019787 2.591503301771407 NW_003726163.1 320442 1614392 5.038016240068406 3.1641487598010345 NW_003726164.1 265648 1332633 5.016536921038367 2.3330099354368317 NW_003726165.1 241365 1228950 5.09166614877882 2.324088256853477 NW_003726166.1 234529 1184768 5.051690835674906 2.2982819243212975 NW_003726167.1 252720 1286972 5.092481798037354 2.8736348989815825 NW_003726168.1 254975 1278255 5.013256201588391 2.956283374072775 NW_003726169.1 226053 1146734 5.07285459604606 2.4051489020602723 NW_003726170.1 223744 1132052 5.059585955377575 2.400509385915509 NW_003726171.1 227140 1133973 4.9923967597076695 2.409560106602754 NW_003726172.1 219672 1095024 4.984813722276849 2.336959122961238 NW_003726173.1 214597 1094928 5.102252128408132 2.3459923431626923 NW_003726174.1 386314 1930860 4.9981621168272445 5.2576192727299444 NW_003726175.1 204342 1022979 5.006210177056111 2.2899945722029447 NW_003726176.1 201724 1011920 5.016358985544605 2.288773379037611 NW_003726177.1 216332 1085362 5.017112586210085 2.705093737505831 NW_003726178.1 200877 1012486 5.040328161013954 2.370674491402684 NW_003726179.1 310654 1519160 4.890199385811868 4.360084913005395 NW_003726180.1 200932 1004831 5.000851034180718 2.3634581364806437 NW_003726181.1 201410 1017554 5.052152326100988 2.4046576821690357 NW_003726182.1 292533 1433145 4.899088307985766 4.171082992022728 NW_003726183.1 192561 961201 4.991670172049377 2.2652923494808754 NW_003726184.1 210134 1069779 5.090937211493618 2.8677778291206284 NW_003726185.1 197844 995087 5.029654677422616 2.7355632829836516 NW_003726186.1 196813 1023302 5.199361830773373 2.749626056540845 NW_003726187.1 180359 908077 5.0348305324380815 2.2889971308179575 NW_003726188.1 210247 1016968 4.837015510328328 3.2205185064988227 NW_003726189.1 177735 913478 5.139550454328073 2.437835057648204 NW_003726190.1 172100 870869 5.060249854735619 2.2945856587655498 NW_003726191.1 166866 826767 4.954676207256122 2.2613668906929503 NW_003726192.1 164926 853214 5.173314092380825 2.3195675364923845 NW_003726193.1 157598 792332 5.027551111054708 2.7254710550321333 NW_003726194.1 143980 720023 5.000854285317406 2.4043127548738608 NW_003726195.1 141074 702297 4.978217105916044 2.415284773396932 NW_003726196.1 139526 689699 4.943157547697203 2.274816654037526 NW_003726197.1 142260 741588 5.212905946857866 2.5546729878141523 NW_003726198.1 138160 687332 4.97489866821077 2.284231389294806 NW_003726199.1 142296 719703 5.057787991229549 2.4994746193035073 NW_003726200.1 133119 666596 5.007519587737288 2.2271816366392603 NW_003726201.1 129748 647664 4.991707001263989 2.2032013935658967 NW_003726202.1 125962 645574 5.125148854416412 2.3911260094406273 NW_003726203.1 127429 637798 5.005124422227279 2.474677811640023 NW_003726204.1 128261 641999 5.005410841955076 2.5201037629844434 NW_003726205.1 131872 653720 4.957231254549867 2.684631515982951 NW_003726206.1 133432 661158 4.955018286468014 2.7796988074814637 NW_003726207.1 119670 597047 4.989111723907412 2.3011553955523194 NW_003726208.1 144750 684310 4.727530224525043 3.2067366047417294 NW_003726209.1 120779 606616 5.022528750859007 2.5813191753977884 NW_003726210.1 115952 575134 4.960104181040431 2.2600356758958413 NW_003726211.1 118237 577502 4.884274803995365 2.530077855787329 NW_003726212.1 111908 556781 4.975345819780534 2.3966294740989302 NW_003726213.1 117332 618205 5.268852486960079 2.748182320382176 NW_003726214.1 111759 558860 5.00058160864002 2.3257729361758113 NW_003726215.1 108801 543907 4.9990992729846235 2.273101752270249 NW_003726216.1 112014 580471 5.182129019586838 2.7648130066471643 NW_003726217.1 106428 539128 5.065659412936445 2.3282444143364707 NW_003726218.1 104912 540605 5.15293770016776 2.134548931797408 NW_003726219.1 104646 520217 4.971207690690519 2.099948482937522 NW_003726220.1 103248 521097 5.047042073454207 2.2597263501596734 NW_003726221.1 129482 624815 4.8254969802752505 3.5007586454635824 NW_003726222.1 118473 589448 4.975378356249947 3.071926360112947 NW_003726223.1 99993 502194 5.022291560409228 2.3600874624265895 NW_003726224.1 109585 550488 5.023388237441256 2.870907631322615 NW_003726225.1 124049 595782 4.8027956694532 3.3707962818394823 NW_003726226.1 99658 496816 4.985209416203416 2.478903941367616 NW_003726227.1 101741 509369 5.0065263757973675 2.642972633915716 NW_003726228.1 97365 493766 5.071288450675294 2.3675685250107015 NW_003726229.1 94395 475769 5.040192806822395 2.3609979481173298 NW_003726230.1 102992 493526 4.791886748485319 2.8196232278127216 NW_003726231.1 95509 474886 4.972159691756798 2.535872326322179 NW_003726232.1 92047 460177 4.999369887122882 2.4001226910386495 NW_003726233.1 87753 448503 5.110970565108885 2.244248752457072 NW_003726234.1 96536 471593 4.885151653269246 3.0857791060747655 NW_003726235.1 86544 432007 4.991761416158255 2.290376653715018 NW_003726236.1 85476 428711 5.015571622443727 2.376590839914173 NW_003726237.1 110512 544161 4.923999203706384 3.713191608992656 NW_003726238.1 83291 415494 4.988462138766494 2.2628093089842296 NW_003726239.1 82459 419106 5.082598624771099 2.257342053942416 NW_003726240.1 81605 420877 5.157490349856014 2.5231358086010007 NW_003726241.1 82380 427517 5.189572711823258 2.495984049304151 NW_003726242.1 102198 490167 4.796248458873951 3.5207141748934885 NW_003726243.1 82108 407664 4.964972962439713 2.4803485006064014 NW_003726244.1 87041 440085 5.056065532335336 2.919168460622692 NW_003726245.1 79722 404694 5.07631519530368 2.2545125595849673 NW_003726246.1 230124 1128273 4.902891484590916 7.340232130645787 NW_003726247.1 78357 395419 5.046377477442985 2.2329100032736777 NW_003726248.1 256406 1260913 4.917642332862726 7.928268164557816 NW_003726249.1 78050 396582 5.081127482383088 2.2617388852994917 NW_003726250.1 81930 407366 4.97212254363481 2.5810680939065307 NW_003726251.1 77100 387922 5.031413748378729 2.289061063871834 NW_003726252.1 77130 386124 5.006145468689226 2.3435421931610283 NW_003726253.1 79078 397502 5.0267078074812215 2.6332075735295946 NW_003726254.1 90550 446100 4.9265599116510215 3.4427424955229675 NW_003726255.1 82767 418763 5.059540638177051 2.9046896212760083 NW_003726256.1 89070 397481 4.4625687661389914 3.1494654315074695 NW_003726257.1 97802 487478 4.984335698656469 3.7195510402626284 NW_003726258.1 79712 398728 5.002107587314332 2.7994931669359326 NW_003726259.1 79581 412482 5.183171862630528 3.004804593774331 NW_003726260.1 73720 375894 5.098941942485078 2.398898196033508 NW_003726261.1 97799 485962 4.968987412959232 3.907982485286419 NW_003726262.1 73171 366305 5.006149977450082 2.2240304052887208 NW_003726263.1 104732 509365 4.863508765229347 3.938372456513105 NW_003726264.1 78935 379184 4.803749920820929 2.7681524214183852 NW_003726265.1 72992 367787 5.03873027181061 2.467765004299486 NW_003726266.1 68721 342583 4.985128272289402 2.2417822665290865 NW_003726267.1 73611 366244 4.975397698713508 2.678366065377303 NW_003726268.1 68272 342296 5.013709866416686 2.3088366984456266 NW_003726269.1 79297 387574 4.887625004729056 3.151286542927702 NW_003726270.1 84443 417864 4.9484741186362395 3.3839408828260336 NW_003726271.1 80679 383984 4.759404553849205 3.292933334663482 NW_003726272.1 68834 350058 5.0855391231077665 2.52612996751747 NW_003726273.1 67496 337499 5.000281498162854 2.4346867420329 NW_003726274.1 66523 335377 5.041519474467478 2.336705801856888 NW_003726275.1 67057 335998 5.010632745276407 2.290143319478453 NW_003726276.1 66195 339893 5.1347231664022965 2.3226812107851456 NW_003726277.1 87584 430756 4.918204238217026 3.706428844074414 NW_003726278.1 84679 386671 4.56631514306971 3.4015790297404203 NW_003726279.1 65840 327596 4.975637910085054 2.19472366561448 NW_003726280.1 65696 332367 5.059166463711642 2.1803406662839704 NW_003726281.1 66021 327291 4.95737719816422 2.348395503470988 NW_003726282.1 67300 337515 5.015081723625557 2.5394668274668737 NW_003726283.1 88153 410371 4.6552130954136555 3.824472565737773 NW_003726284.1 92437 451022 4.8792366692990905 4.1564403298036225 NW_003726285.1 70351 344682 4.89946127276087 2.897339129627591 NW_003726286.1 64646 330731 5.11603192772948 2.460292605753904 NW_003726287.1 69126 341409 4.9389375922228975 2.8168682463499874 NW_003726288.1 227674 1028991 4.519580628442422 7.752994208235013 NW_003726289.1 64123 325191 5.071362849523572 2.4307657742385587 NW_003726290.1 61944 310183 5.007474493090533 2.229559487056155 NW_003726291.1 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