BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_no_error_hi_variance/alignment/1X_no_error_hi_variance.sorted.bam outfile = results/1X_no_error_hi_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 = 16,073,088 number of mapped reads = 16,073,088 (100%) number of supplementary alignments = 105 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,036,544 number of mapped paired reads (second in pair) = 8,036,544 number of mapped paired reads (both in pair) = 16,073,088 number of mapped paired reads (singletons) = 0 number of mapped bases = 2,406,317,998 bp number of sequenced bases = 2,398,448,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,880 duplication rate = 0.38% >>>>>>> Insert size mean insert size = 408.4591 std insert size = 40,198.8007 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 30.9717 >>>>>>> ACTG content number of A's = 699,929,755 bp (29.18%) number of C's = 499,254,589 bp (20.82%) number of T's = 699,990,278 bp (29.19%) number of G's = 499,270,103 bp (20.82%) number of N's = 4,066 bp (0%) GC percentage = 41.63% >>>>>>> Mismatches and indels general error rate = 0.0345 number of mismatches = 75,260,957 number of insertions = 5,465,516 mapped reads with insertion percentage = 29.08% number of deletions = 5,487,836 mapped reads with deletion percentage = 29.11% homopolymer indels = 28.22% >>>>>>> Coverage mean coverageData = 0.9981X std coverageData = 1.0182X There is a 62.18% of reference with a coverageData >= 1X There is a 26.34% of reference with a coverageData >= 2X There is a 8.32% of reference with a coverageData >= 3X There is a 2.1% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.01% 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 122529792 0.9987855031332434 1.0143790761674698 NC_006584.3 85426708 85480758 1.0006327061087266 1.0176287813069032 NC_006585.3 91889043 91801486 0.9990471442824799 1.0157383624961487 NC_006586.3 88276631 88185136 0.998963542231239 1.0155381797553118 NC_006587.3 88915250 88773406 0.9984047280978234 1.0172082241604545 NC_006588.3 77573801 77452231 0.99843284719283 1.0159599182670633 NC_006589.3 80974532 80844287 0.9983915313027064 1.0168297507046047 NC_006590.3 74330416 74242097 0.9988118053852948 1.0152251784852733 NC_006591.3 61074082 61079281 1.0000851261260055 1.0174292796223516 NC_006592.3 69331447 69202621 0.9981418821389954 1.017093472650442 NC_006593.3 74389097 74264051 0.9983190278543104 1.0151873813883723 NC_006594.3 72498081 72348046 0.997930496946533 1.0143416993448844 NC_006595.3 63241923 63132179 0.9982646953983357 1.0158979773699937 NC_006596.3 60966679 60866361 0.9983545437992448 1.0149917557349424 NC_006597.3 64190966 64063440 0.9980133341504784 1.0143167586509767 NC_006598.3 59632846 59636408 1.0000597321818248 1.0191918781577065 NC_006599.3 64289059 64191963 0.9984896963571982 1.0131612224741207 NC_006600.3 55844845 55767153 0.9986087883313133 1.0185458093898323 NC_006601.3 53741614 53641299 0.9981333831916548 1.0170928334499496 NC_006602.3 58134056 58009241 0.9978529796716747 1.0174223990483833 NC_006603.3 50858623 50783957 0.9985318910423508 1.0138795183591187 NC_006604.3 61439934 61305596 0.9978135067658113 1.0143827113106585 NC_006605.3 52294480 52147327 0.9971860701167695 1.0139871196183479 NC_006606.3 47698779 47626268 0.9984798143365473 1.0159867559546651 NC_006607.3 51628933 51541117 0.9982990932622993 1.015254044795313 NC_006608.3 38964690 38914655 0.9987158886674063 1.0176287981766103 NC_006609.3 45876710 45786506 0.9980337735639718 1.0148138465868124 NC_006610.3 41182112 41106455 0.9981628674119482 1.0137990101817618 NC_006611.3 41845238 41766639 0.9981216739644305 1.015195720531682 NC_006612.3 40214260 40135799 0.9980489259282652 1.0131615225268045 NC_006613.3 39895921 39805134 0.9977244039559834 1.0144716232593558 NC_006614.3 38810281 38731352 0.9979662863043944 1.0140754909441925 NC_006615.3 31377067 31321126 0.9982171373761608 1.012425649293738 NC_006616.3 42124431 42058720 0.998440073884915 1.0163027087966652 NC_006617.3 26524999 26469217 0.9978970027482376 1.0159175309228854 NC_006618.3 30810995 30741042 0.9977296091865907 1.0133162326224547 NC_006619.3 30902991 30834437 0.9977816386769811 1.0160228071439872 NC_006620.3 23914537 23862958 0.9978431947062157 1.0154734923329727 NC_006621.3 123869142 123644384 0.9981855206521089 1.017756160518049 NW_003726127.1 2660953 2673974 1.0048933596346872 1.0341481293705244 NW_003726128.1 1881673 1857246 0.9870184670769044 1.068504493591887 NW_003726129.1 1415205 1416074 1.0006140453149897 1.0588795375167341 NW_003726130.1 1067467 1071003 1.003312514578905 1.1030824166026247 NW_003726131.1 866315 874184 1.009083301108719 1.0292821211557472 NW_003726132.1 881102 895115 1.0159039475565825 1.078401002222583 NW_003726133.1 822601 822048 0.9993277421252831 1.0384873995963262 NW_003726134.1 741967 739283 0.9963825884439604 1.0044815057906702 NW_003726135.1 745551 737685 0.9894494139233936 1.1284777033080382 NW_003726136.1 602611 605541 1.0048621747694615 1.0052202234134138 NW_003726137.1 573630 575738 1.003674842668619 1.0380485934247257 NW_003726138.1 666183 669528 1.0050211428391298 1.102358674796727 NW_003726139.1 557017 556072 0.9983034629104677 1.040771303398088 NW_003726140.1 510604 517095 1.0127123955158988 1.0146715814593112 NW_003726141.1 497093 501474 1.0088132401783971 1.0257981637384248 NW_003726142.1 492630 496520 1.0078963928303188 1.0677899075679214 NW_003726143.1 577062 572550 0.9921810827952628 1.144169969241598 NW_003726144.1 561270 550772 0.9812959894524916 1.132679297228291 NW_003726145.1 407330 405382 0.9952176368055385 1.0068872134935913 NW_003726146.1 405216 403932 0.9968313195925136 0.9995313605120142 NW_003726147.1 508668 500935 0.9847975496787689 1.1276896797637757 NW_003726148.1 540093 525995 0.9738970880940875 1.2055672371562944 NW_003726149.1 448434 446985 0.9967687552683338 1.1108711303465792 NW_003726150.1 377800 377625 0.9995367919534145 1.0413268062758108 NW_003726151.1 384880 387129 1.0058433797547288 1.0572371642683331 NW_003726152.1 367143 369873 1.0074357947720642 1.0595723620055137 NW_003726153.1 399987 398587 0.996499886246303 1.0975607350305083 NW_003726154.1 376204 379381 1.0084448862851005 1.0310654873070564 NW_003726155.1 416178 413199 0.9928420051035854 1.1184629719114814 NW_003726156.1 365470 365137 0.9990888445016006 1.0505153809985375 NW_003726157.1 322752 326579 1.0118574013484036 1.0355057753013948 NW_003726158.1 320591 325493 1.0152905103387182 1.0145291165033632 NW_003726159.1 310270 307733 0.9918232507171173 1.0287415330844434 NW_003726160.1 433650 417669 0.9631476997578693 1.2128043577913779 NW_003726161.1 273228 278656 1.019866192337535 1.0283872401197145 NW_003726162.1 281659 288021 1.022587597058855 1.0540688368225009 NW_003726163.1 320442 318917 0.9952409484399672 1.1146932795997375 NW_003726164.1 265648 265308 0.9987201108233452 1.0265466878856389 NW_003726165.1 241365 241359 0.9999751413833821 1.0279441638337465 NW_003726166.1 234529 238339 1.0162453257379684 1.0053545791192922 NW_003726167.1 252720 253673 1.0037709718265273 1.0694537287971333 NW_003726168.1 254975 258318 1.0131110893224826 1.114149849216254 NW_003726169.1 226053 228308 1.0099755367104175 1.0252902757588884 NW_003726170.1 223744 226530 1.0124517305491991 1.0256477230844239 NW_003726171.1 227140 229886 1.012089460244783 1.0612203000412417 NW_003726172.1 219672 228801 1.0415574128700973 1.0371518043216836 NW_003726173.1 214597 214644 1.0002190151772858 1.0258255798546136 NW_003726174.1 386314 383959 0.9939039227157183 1.3912912790062413 NW_003726175.1 204342 203252 0.9946658053655146 0.9887128757814713 NW_003726176.1 201724 204881 1.015650096171006 1.0548068041276382 NW_003726177.1 216332 223460 1.0329493556200655 1.0611348320835885 NW_003726178.1 200877 203222 1.0116738103416518 1.0449403894868399 NW_003726179.1 310654 298444 0.9606958223618559 1.2504046035715422 NW_003726180.1 200932 198440 0.9875977942786615 1.006781483740838 NW_003726181.1 201410 203785 1.0117918673352861 1.0348721227013125 NW_003726182.1 292533 290616 0.9934468931710269 1.2191167135386336 NW_003726183.1 192561 194548 1.0103188080660155 1.0044514526449708 NW_003726184.1 210134 218023 1.0375427108416535 1.056910592998011 NW_003726185.1 197844 200281 1.0123177857301713 1.0429672604638809 NW_003726186.1 196813 203389 1.0334124270246376 1.0742257423224957 NW_003726187.1 180359 183165 1.0155578596022377 1.0094759307970633 NW_003726188.1 210247 203011 0.9655833376932845 1.1056623910833376 NW_003726189.1 177735 182113 1.024632177117619 1.0246413540364632 NW_003726190.1 172100 174864 1.0160604299825682 1.0462519859252626 NW_003726191.1 166866 168799 1.0115841453621468 1.062202007547212 NW_003726192.1 164926 167545 1.0158798491444647 1.0389864869153802 NW_003726193.1 157598 155628 0.9874998413685453 1.0625890011199204 NW_003726194.1 143980 143805 0.9987845534101959 1.0174532063082657 NW_003726195.1 141074 140517 0.9960517175383132 1.0206640358432653 NW_003726196.1 139526 138446 0.9922595071886243 1.0310038813168723 NW_003726197.1 142260 145312 1.021453676367215 1.023238662981086 NW_003726198.1 138160 136928 0.9910828025477707 1.0390192624482668 NW_003726199.1 142296 140079 0.9844198009782426 1.0385912687591352 NW_003726200.1 133119 132608 0.996161329336909 0.9948777113133901 NW_003726201.1 129748 130058 1.0023892468477356 1.0398626663248818 NW_003726202.1 125962 134743 1.0697115002937394 1.081860872132805 NW_003726203.1 127429 127476 1.0003688328402482 1.0646172583443485 NW_003726204.1 128261 131523 1.0254325165093052 1.0406795047148918 NW_003726205.1 131872 133347 1.0111850885707352 1.067192561551718 NW_003726206.1 133432 137572 1.0310270399904071 1.1165672235003283 NW_003726207.1 119670 122190 1.0210579092504386 1.0271771198887873 NW_003726208.1 144750 134102 0.9264386873920553 1.071560978912013 NW_003726209.1 120779 119225 0.9871335248677336 1.0319845674785832 NW_003726210.1 115952 118864 1.025113840209742 0.9865023224600986 NW_003726211.1 118237 120058 1.0154012703299307 1.0465948251958865 NW_003726212.1 111908 111171 0.9934142331200629 1.009762028084952 NW_003726213.1 117332 121787 1.0379691814679712 1.0507209159112878 NW_003726214.1 111759 111770 1.0000984260775418 1.0325290405306664 NW_003726215.1 108801 114038 1.0481337487706914 1.069712408038279 NW_003726216.1 112014 113525 1.0134893852554145 1.0517636910843318 NW_003726217.1 106428 112231 1.054525124967114 1.0454534465310512 NW_003726218.1 104912 107194 1.0217515632148848 0.9767774848938691 NW_003726219.1 104646 104197 0.9957093438831871 0.9848933975968306 NW_003726220.1 103248 104711 1.01416976600031 1.0357379564627502 NW_003726221.1 129482 130970 1.011491944826308 1.1285592187661502 NW_003726222.1 118473 120401 1.0162737501371621 1.119584215988687 NW_003726223.1 99993 102082 1.0208914624023682 1.019742234241584 NW_003726224.1 109585 112231 1.0241456403704887 1.1104692769120281 NW_003726225.1 124049 115838 0.9338084144168837 1.1306000805634053 NW_003726226.1 99658 95913 0.9624214814666159 0.9902663115982473 NW_003726227.1 101741 102072 1.003253359019471 1.0176546553009684 NW_003726228.1 97365 98995 1.0167411287423611 1.0201955377622443 NW_003726229.1 94395 94677 1.0029874463689814 1.019212701565838 NW_003726230.1 102992 93961 0.9123135777536119 1.0257678105449342 NW_003726231.1 95509 91964 0.9628830790815526 1.0047225403063094 NW_003726232.1 92047 93448 1.0152204851869153 1.044268350698819 NW_003726233.1 87753 89971 1.025275489157066 1.0060396416699606 NW_003726234.1 96536 93988 0.9736057014999586 1.099444423949345 NW_003726235.1 86544 84124 0.9720373451654649 1.0017503546938016 NW_003726236.1 85476 86585 1.0129744021713698 0.9821236555098275 NW_003726237.1 110512 102330 0.9259627913710728 1.1392936475021513 NW_003726238.1 83291 85013 1.020674502647345 1.0378433699845027 NW_003726239.1 82459 84230 1.0214773402539443 1.0174624063079056 NW_003726240.1 81605 81560 0.9994485632007842 1.102573990034641 NW_003726241.1 82380 83717 1.0162296673949989 1.104519496038311 NW_003726242.1 102198 100670 0.985048631088671 1.198785101644279 NW_003726243.1 82108 82337 1.002789009597116 1.006579627709923 NW_003726244.1 87041 85101 0.9777116531289852 1.098557427014115 NW_003726245.1 79722 80234 1.0064223175534983 1.052247678265466 NW_003726246.1 230124 225651 0.9805626531782865 1.7078461755205716 NW_003726247.1 78357 79069 1.0090866163839862 1.0098004938345495 NW_003726248.1 256406 248220 0.9680740700295625 1.8179322996366771 NW_003726249.1 78050 81310 1.0417680973734786 1.063186616987523 NW_003726250.1 81930 81284 0.9921152203100208 1.0366213265119375 NW_003726251.1 77100 78000 1.0116731517509727 1.0162649460112017 NW_003726252.1 77130 76603 0.9931673797484766 1.001587830649651 NW_003726253.1 79078 80276 1.015149599129973 1.0664639805419338 NW_003726254.1 90550 85897 0.9486140254003314 1.0886613941197076 NW_003726255.1 82767 82659 0.9986951321178731 1.091127982702854 NW_003726256.1 89070 79918 0.8972493544403278 1.0652307791807307 NW_003726257.1 97802 96451 0.9861863765567166 1.1542053979742997 NW_003726258.1 79712 79772 1.0007527097551183 1.0979731521970155 NW_003726259.1 79581 85139 1.0698407911436147 1.1580691208741192 NW_003726260.1 73720 73726 1.0000813890396094 1.0417885866330066 NW_003726261.1 97799 91923 0.9399175860693872 1.142826324616791 NW_003726262.1 73171 73322 1.0020636590999166 1.0184128296558028 NW_003726263.1 104732 103409 0.9873677577053813 1.219372869131083 NW_003726264.1 78935 69755 0.8837017799455248 1.0177043172556528 NW_003726265.1 72992 77155 1.0570336475230162 1.0457062453987855 NW_003726266.1 68721 72045 1.0483694940411228 1.067723967739545 NW_003726267.1 73611 72457 0.984322995204521 1.001595433183291 NW_003726268.1 68272 68393 1.0017723224748067 0.9725441499990329 NW_003726269.1 79297 79034 0.9966833549819035 1.019368791937916 NW_003726270.1 84443 82460 0.9765167035751927 1.1231559425798867 NW_003726271.1 80679 74324 0.9212310514508112 1.0760448147958979 NW_003726272.1 68834 72113 1.0476363425051574 1.1337695576346967 NW_003726273.1 67496 67303 0.9971405712931136 1.013270798821675 NW_003726274.1 66523 65546 0.9853133502698315 1.0797463326235617 NW_003726275.1 67057 68143 1.0161951772372757 1.0567554267483175 NW_003726276.1 66195 64668 0.9769317924314526 1.0003483971711693 NW_003726277.1 87584 82412 0.9409481183777859 1.0959291651479108 NW_003726278.1 84679 75966 0.8971055397442105 1.1090801762753084 NW_003726279.1 65840 66198 1.0054374240583233 1.003166709024418 NW_003726280.1 65696 66998 1.0198185582075012 1.0619988473132036 NW_003726281.1 66021 65870 0.9977128489420033 1.055871971310631 NW_003726282.1 67300 67338 1.0005646359583953 1.0252040809938352 NW_003726283.1 88153 87832 0.9963586037911358 1.199154971231861 NW_003726284.1 92437 87162 0.9429341064725164 1.1881530926737172 NW_003726285.1 70351 72436 1.0296371053716364 1.0761493635812733 NW_003726286.1 64646 68337 1.057095566624385 1.1143529278554378 NW_003726287.1 69126 68259 0.98745768596476 1.0664210582472227 NW_003726288.1 227674 204316 0.8974059400722085 1.7953391346311742 NW_003726289.1 64123 62023 0.9672504405595496 1.03032326529098 NW_003726290.1 61944 61740 0.996706702828361 0.9731244912401006 NW_003726291.1 62414 61240 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