BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_med_error_med_variance/alignment/1X_med_error_med_variance.sorted.bam outfile = results/1X_med_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 = 16,073,088 number of mapped reads = 16,073,088 (100%) number of supplementary alignments = 20 (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 = 2,410,206,274 bp number of sequenced bases = 2,408,596,855 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,570 duplication rate = 0.34% >>>>>>> Insert size mean insert size = 389.1821 std insert size = 45,464.72 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 31.7253 >>>>>>> ACTG content number of A's = 706,098,333 bp (29.32%) number of C's = 500,229,053 bp (20.77%) number of T's = 704,137,350 bp (29.23%) number of G's = 498,127,998 bp (20.68%) number of N's = 4,121 bp (0%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0168 number of mismatches = 38,987,037 number of insertions = 1,123,852 mapped reads with insertion percentage = 6.77% number of deletions = 1,131,785 mapped reads with deletion percentage = 6.81% homopolymer indels = 28.44% >>>>>>> Coverage mean coverageData = 0.9997X std coverageData = 1.0194X There is a 62.37% of reference with a coverageData >= 1X There is a 26.48% of reference with a coverageData >= 2X There is a 8.38% of reference with a coverageData >= 3X There is a 2.12% 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 122767353 1.0007219504170994 1.0171567159702013 NC_006584.3 85426708 85675186 1.0029086687971167 1.0191407084758102 NC_006585.3 91889043 91952612 1.000691801741803 1.0162508736105789 NC_006586.3 88276631 88357934 1.0009210025244393 1.0169943678587305 NC_006587.3 88915250 88933327 1.0002033059570772 1.0181482018627288 NC_006588.3 77573801 77584961 1.0001438630034385 1.0189220618410295 NC_006589.3 80974532 80990641 1.0001989390935906 1.018322471522878 NC_006590.3 74330416 74344284 1.0001865723447585 1.015994028394665 NC_006591.3 61074082 61179395 1.0017243484724012 1.0188261518483104 NC_006592.3 69331447 69306609 0.9996417498685698 1.0162564233811746 NC_006593.3 74389097 74374433 0.9998028743378885 1.0165157711038086 NC_006594.3 72498081 72444922 0.9992667530055037 1.0171690501275847 NC_006595.3 63241923 63226488 0.9997559372127252 1.0176173341405708 NC_006596.3 60966679 60953136 0.9997778622647299 1.0158234630539398 NC_006597.3 64190966 64166240 0.9996148056098735 1.0167053576769705 NC_006598.3 59632846 59705981 1.0012264214255344 1.0165268903266778 NC_006599.3 64289059 64309646 1.000320225561242 1.0179473519426359 NC_006600.3 55844845 55848568 1.000066666851703 1.0181589377876996 NC_006601.3 53741614 53729746 0.9997791655457166 1.0183831501116547 NC_006602.3 58134056 58099694 0.9994089178983142 1.0172841376924109 NC_006603.3 50858623 50836686 0.9995686670478672 1.0175515970155198 NC_006604.3 61439934 61393509 0.9992443839539281 1.0145624331650454 NC_006605.3 52294480 52257023 0.9992837293725839 1.0173172533440726 NC_006606.3 47698779 47700141 1.000028554190035 1.0188904678607835 NC_006607.3 51628933 51606012 0.9995560435076201 1.0175659149915446 NC_006608.3 38964690 38988175 1.0006027251852896 1.0181392346527134 NC_006609.3 45876710 45853338 0.9994905476002965 1.0157146762148395 NC_006610.3 41182112 41164631 0.9995755195848139 1.0162858155460153 NC_006611.3 41845238 41825722 0.9995336147926797 1.0137414127945044 NC_006612.3 40214260 40187666 0.9993386922947233 1.0152225292569952 NC_006613.3 39895921 39882703 0.9996686879342879 1.0169830857449267 NC_006614.3 38810281 38788901 0.9994491150424806 1.010312477718758 NC_006615.3 31377067 31365140 0.9996198816160861 1.0137001361061115 NC_006616.3 42124431 42100458 0.999430900324802 1.0177172058981832 NC_006617.3 26524999 26505564 0.9992672949770893 1.0160803644423062 NC_006618.3 30810995 30788863 0.9992816849958919 1.0154347899305614 NC_006619.3 30902991 30878785 0.9992167101236252 1.0182641400301848 NC_006620.3 23914537 23905221 0.9996104461482989 1.0154230334020617 NC_006621.3 123869142 123833507 0.9997123173744111 1.0169197955913534 NW_003726127.1 2660953 2662792 1.000691105780523 1.029914635682989 NW_003726128.1 1881673 1894511 1.0068226519698162 1.0779424150596408 NW_003726129.1 1415205 1415394 1.0001335495564248 1.0646490741429058 NW_003726130.1 1067467 1072077 1.0043186346744208 1.0890793396439913 NW_003726131.1 866315 864822 0.998276608393021 1.0093257244913028 NW_003726132.1 881102 881619 1.0005867652099303 1.0435850122118508 NW_003726133.1 822601 824497 1.0023048841418865 1.0411624718764818 NW_003726134.1 741967 747389 1.0073076026292274 1.0260426389077968 NW_003726135.1 745551 748729 1.0042626191903705 1.1243002616491078 NW_003726136.1 602611 604952 1.0038847614796278 1.0054618964109516 NW_003726137.1 573630 570552 0.9946341718529366 1.018864616763462 NW_003726138.1 666183 665052 0.9983022682956485 1.126885649552496 NW_003726139.1 557017 560262 1.0058256749793992 1.0668493865538777 NW_003726140.1 510604 518476 1.0154170355108851 1.0342436568220035 NW_003726141.1 497093 500458 1.0067693570418412 1.0354034787516553 NW_003726142.1 492630 493948 1.0026754359255425 1.042165856029345 NW_003726143.1 577062 580879 1.0066145405519684 1.147424761704452 NW_003726144.1 561270 563157 1.0033620182799723 1.12521207073379 NW_003726145.1 407330 405504 0.9955171482581691 1.0112863236132048 NW_003726146.1 405216 405718 1.0012388454552634 1.0487082147722722 NW_003726147.1 508668 507075 0.9968682913019887 1.1520102723614227 NW_003726148.1 540093 545210 1.0094742942419177 1.213261966000754 NW_003726149.1 448434 448553 1.0002653679248228 1.133749958344214 NW_003726150.1 377800 380613 1.0074457384859714 1.0635250395946614 NW_003726151.1 384880 381162 0.9903398461858242 1.060122039276847 NW_003726152.1 367143 373106 1.0162416279215456 1.0332465762713414 NW_003726153.1 399987 398232 0.9956123574016156 1.0778871055159724 NW_003726154.1 376204 371583 0.9877167706882436 1.0648524559212984 NW_003726155.1 416178 411542 0.9888605356361941 1.1336276843300401 NW_003726156.1 365470 366394 1.0025282512928557 1.0989735588837046 NW_003726157.1 322752 328699 1.018425912155463 1.0244446406924859 NW_003726158.1 320591 321795 1.003755563942843 1.0249516984948983 NW_003726159.1 310270 308569 0.9945176781512876 1.0197886232394242 NW_003726160.1 433650 425564 0.9813536261962412 1.19896636943595 NW_003726161.1 273228 277080 1.0140981158592823 1.0300590792733657 NW_003726162.1 281659 288532 1.024401847624255 1.0370841408546925 NW_003726163.1 320442 326222 1.0180375855849109 1.1131276710776665 NW_003726164.1 265648 264137 0.9943120219237487 1.0095945185000754 NW_003726165.1 241365 249183 1.0323907774532348 1.0721250712759667 NW_003726166.1 234529 239318 1.0204196495955724 1.009109524098839 NW_003726167.1 252720 252480 0.9990503323836657 1.0863889220024656 NW_003726168.1 254975 256968 1.0078164525933915 1.0668375160377384 NW_003726169.1 226053 222150 0.982734137569508 1.00588559285623 NW_003726170.1 223744 226955 1.014351222826087 1.0094248806427482 NW_003726171.1 227140 234184 1.0310117108391301 1.0381192657395648 NW_003726172.1 219672 218664 0.9954113405440839 1.0150098110963532 NW_003726173.1 214597 215343 1.0034762834522384 1.028987201053887 NW_003726174.1 386314 384753 0.9959592455877861 1.4069979007479534 NW_003726175.1 204342 209644 1.0259466972037075 1.039194024811396 NW_003726176.1 201724 209024 1.036188058932006 1.0307336905611426 NW_003726177.1 216332 219267 1.0135671098126953 1.0817932427398824 NW_003726178.1 200877 200607 0.9986558939052256 0.9911526987678854 NW_003726179.1 310654 307695 0.9904749335273326 1.23936099624418 NW_003726180.1 200932 200371 0.9972080106702765 1.0345005918472807 NW_003726181.1 201410 204852 1.0170895188918128 1.0117697639836658 NW_003726182.1 292533 283858 0.9703452260086897 1.1849692481982825 NW_003726183.1 192561 190099 0.9872144411381328 0.987644620798666 NW_003726184.1 210134 212589 1.0116830213102115 1.0706539209796873 NW_003726185.1 197844 199769 1.0097298881947392 1.0688370832167453 NW_003726186.1 196813 215640 1.0956593314466017 1.1355227411294664 NW_003726187.1 180359 185666 1.0294246475085802 1.0683168982871039 NW_003726188.1 210247 203021 0.9656309007976333 1.091925822841127 NW_003726189.1 177735 189170 1.0643373561763299 1.0602959771441844 NW_003726190.1 172100 174571 1.014357931435212 1.0324130173766972 NW_003726191.1 166866 167099 1.0013963299893327 0.9989149136135008 NW_003726192.1 164926 170358 1.0329359834107419 0.9868226479312127 NW_003726193.1 157598 156840 0.9951902942930748 1.059680330865025 NW_003726194.1 143980 143939 0.9997152382275316 1.0326013829408802 NW_003726195.1 141074 140928 0.9989650821554645 1.0500256195944477 NW_003726196.1 139526 141233 1.0122342789157577 0.9803061770243585 NW_003726197.1 142260 138538 0.9738366371432589 1.002518958023364 NW_003726198.1 138160 137334 0.9940214244354372 0.9706472051413157 NW_003726199.1 142296 144531 1.015706695901501 1.051171789259231 NW_003726200.1 133119 132267 0.9935997115362946 1.008446369160562 NW_003726201.1 129748 130486 1.00568794894719 1.0789525897191439 NW_003726202.1 125962 131928 1.047363490576523 1.03314425485575 NW_003726203.1 127429 128683 1.0098407740781141 1.0497912192672767 NW_003726204.1 128261 129272 1.0078823648653916 1.0512342348482235 NW_003726205.1 131872 133142 1.0096305508371755 1.0614656978639996 NW_003726206.1 133432 137674 1.0317914743090113 1.1001463102287525 NW_003726207.1 119670 121755 1.0174229130107797 0.9968956486567742 NW_003726208.1 144750 138301 0.9554473229706391 1.0982201501193705 NW_003726209.1 120779 125070 1.0355276993517084 1.0335649223857872 NW_003726210.1 115952 112691 0.9718762936387471 0.9831123058116147 NW_003726211.1 118237 110975 0.9385809856474707 1.0061295422700052 NW_003726212.1 111908 110952 0.9914572684705294 1.0121444936814497 NW_003726213.1 117332 122037 1.0400998874987215 1.0338749402541079 NW_003726214.1 111759 111865 1.0009484694744941 1.0333734300929438 NW_003726215.1 108801 108264 0.9950643835994154 1.0249496311408144 NW_003726216.1 112014 114262 1.0200689199564341 1.0450820457948007 NW_003726217.1 106428 108282 1.017420227759612 1.0488590266152247 NW_003726218.1 104912 108292 1.0322174775049566 1.050762881160238 NW_003726219.1 104646 103160 0.9857997438984768 1.0080822839325674 NW_003726220.1 103248 101940 0.9873314737331473 1.092136319027322 NW_003726221.1 129482 128089 0.9892417478877373 1.1529876230759593 NW_003726222.1 118473 119321 1.0071577490229842 1.1087880561568866 NW_003726223.1 99993 99878 0.9988499194943646 1.030534502763875 NW_003726224.1 109585 107949 0.9850709494912625 1.0636637354864975 NW_003726225.1 124049 117022 0.9433530298511072 1.109584358777763 NW_003726226.1 99658 100186 1.0052981195689257 1.053329175473514 NW_003726227.1 101741 102007 1.0026144818706324 1.0453288845860287 NW_003726228.1 97365 101770 1.0452421301288963 1.037975651680914 NW_003726229.1 94395 94478 1.000879283860374 1.005077732354457 NW_003726230.1 102992 100027 0.9712113562218425 1.032449633467911 NW_003726231.1 95509 93578 0.9797820100723492 1.0221896191268662 NW_003726232.1 92047 89690 0.9743935163557748 0.9819180487566632 NW_003726233.1 87753 89641 1.0215149339623717 1.0166194306599334 NW_003726234.1 96536 100139 1.0373228640092815 1.1190132731489584 NW_003726235.1 86544 91176 1.0535219079312257 1.0274451612083346 NW_003726236.1 85476 84514 0.9887453788197856 0.99359906909517 NW_003726237.1 110512 112452 1.0175546546981322 1.1912576960778813 NW_003726238.1 83291 83398 1.0012846526035226 1.0766955448176916 NW_003726239.1 82459 83365 1.0109872785262979 1.030456665479322 NW_003726240.1 81605 83693 1.02558666748361 1.0513248539015854 NW_003726241.1 82380 82740 1.0043699927166787 0.9927133167874298 NW_003726242.1 102198 98949 0.9682087712088299 1.1284653125471675 NW_003726243.1 82108 82472 1.0044331855604813 1.0427994463429036 NW_003726244.1 87041 86930 0.998724738916143 1.0780840713386663 NW_003726245.1 79722 82530 1.0352223978324677 1.0755402016573805 NW_003726246.1 230124 224035 0.973540352157967 1.7139589728798166 NW_003726247.1 78357 77394 0.9877100960986255 1.0524482929918237 NW_003726248.1 256406 250450 0.9767712144021591 1.8222692119937949 NW_003726249.1 78050 78556 1.0064830237027547 1.0497815824457055 NW_003726250.1 81930 81262 0.9918466984010741 1.0246913168616554 NW_003726251.1 77100 77681 1.0075356679636835 1.0644558323477837 NW_003726252.1 77130 76180 0.9876831323739141 1.0769277074160808 NW_003726253.1 79078 83074 1.0505323857457194 1.0426198532297364 NW_003726254.1 90550 83111 0.9178464936499172 1.0860128614651232 NW_003726255.1 82767 83394 1.007575482982348 1.0608520567131614 NW_003726256.1 89070 80359 0.9022005164477377 1.017935608933752 NW_003726257.1 97802 97420 0.9960941494038976 1.1337836260703573 NW_003726258.1 79712 79764 1.000652348454436 1.0414919559341678 NW_003726259.1 79581 81230 1.0207210263756423 1.1745590484939674 NW_003726260.1 73720 74966 1.0169017905588713 1.0701257473808254 NW_003726261.1 97799 98024 1.0023006370208285 1.2211255677157065 NW_003726262.1 73171 72601 0.9922100285632286 0.9828347506052422 NW_003726263.1 104732 102894 0.9824504449451934 1.2401316203930857 NW_003726264.1 78935 71681 0.9081016025844049 1.0205448336396983 NW_003726265.1 72992 77412 1.0605545813239807 1.1093612915569862 NW_003726266.1 68721 69560 1.0122087862516553 0.9684755719538404 NW_003726267.1 73611 66563 0.9042534403825515 1.0266131578949282 NW_003726268.1 68272 68385 1.0016551441293648 1.0331462166460437 NW_003726269.1 79297 75897 0.9571232202983719 1.1159336901011219 NW_003726270.1 84443 89377 1.0584299468280378 1.1982781298788583 NW_003726271.1 80679 76734 0.9511025173837058 1.1159468776271215 NW_003726272.1 68834 67773 0.9845861057035767 1.0131006287183715 NW_003726273.1 67496 67155 0.9949478487614081 1.0178278172070931 NW_003726274.1 66523 67490 1.0145363257820603 1.022610118147476 NW_003726275.1 67057 67804 1.0111397766079604 0.9894882489249728 NW_003726276.1 66195 66569 1.0056499735629578 1.0076547698374334 NW_003726277.1 87584 86886 0.992030507855316 1.185961575660053 NW_003726278.1 84679 76766 0.9065529824395658 1.0659946136951834 NW_003726279.1 65840 63573 0.9655680437424058 0.8921994347876007 NW_003726280.1 65696 67785 1.0317979785679494 1.061419071958598 NW_003726281.1 66021 66311 1.0043925417670134 1.0406540371663 NW_003726282.1 67300 67167 0.9980237741456166 1.1025881359077978 NW_003726283.1 88153 85538 0.970335666398194 1.2125643674141706 NW_003726284.1 92437 90751 0.9817605504289408 1.2373103108274988 NW_003726285.1 70351 69555 0.9886853065343776 1.0903160139211552 NW_003726286.1 64646 64463 0.9971691984036135 0.9988952985942557 NW_003726287.1 69126 69929 1.0116164684778521 1.0746202052361686 NW_003726288.1 227674 204870 0.8998392438310918 1.7600670073644802 NW_003726289.1 64123 66555 1.0379271088377025 1.0834680899541742 NW_003726290.1 61944 61933 0.9998224202505489 1.0334079885643073 NW_003726291.1 62414 62374 0.9993591181465696 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