BamQC report ----------------------------------- >>>>>>> Input bam file = results/0.5X_no_error_med_variance/alignment/0.5X_no_error_med_variance.sorted.bam outfile = results/0.5X_no_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 = 8,036,542 number of mapped reads = 8,036,542 (100%) number of supplementary alignments = 2 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,018,271 number of mapped paired reads (second in pair) = 4,018,271 number of mapped paired reads (both in pair) = 8,036,542 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,205,344,796 bp number of sequenced bases = 1,204,538,370 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,711 duplication rate = 0.17% >>>>>>> Insert size mean insert size = 349.9826 std insert size = 49.9825 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 32.3065 >>>>>>> ACTG content number of A's = 353,131,739 bp (29.32%) number of C's = 249,129,684 bp (20.68%) number of T's = 353,149,982 bp (29.32%) number of G's = 249,124,793 bp (20.68%) number of N's = 2,172 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 7,640,343 number of insertions = 564,331 mapped reads with insertion percentage = 6.8% number of deletions = 568,243 mapped reads with deletion percentage = 6.84% homopolymer indels = 28.67% >>>>>>> Coverage mean coverageData = 0.4999X std coverageData = 0.7185X There is a 38.81% of reference with a coverageData >= 1X There is a 9.28% of reference with a coverageData >= 2X There is a 1.62% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 61403554 0.5005230040385549 0.7177908682299765 NC_006584.3 85426708 42870218 0.501836240722281 0.7187644073460189 NC_006585.3 91889043 45973856 0.5003192382795847 0.7172445278429942 NC_006586.3 88276631 44181601 0.5004903392835642 0.7168437181571796 NC_006587.3 88915250 44467551 0.5001116343934252 0.7183071391293722 NC_006588.3 77573801 38807588 0.5002666815307916 0.7193289116967946 NC_006589.3 80974532 40501023 0.500169892923864 0.717438006613198 NC_006590.3 74330416 37181199 0.5002151340038242 0.7176179560202655 NC_006591.3 61074082 30604256 0.5011005486746407 0.7188970011319598 NC_006592.3 69331447 34661349 0.49993690453337863 0.7183431251490217 NC_006593.3 74389097 37189255 0.49992884037831514 0.7169077118532534 NC_006594.3 72498081 36230145 0.4997393655150679 0.7170075493749434 NC_006595.3 63241923 31622232 0.5000200895219458 0.717679503305496 NC_006596.3 60966679 30483751 0.5000067495885745 0.7183806472746489 NC_006597.3 64190966 32082627 0.49979972259647876 0.7187361603324103 NC_006598.3 59632846 29859098 0.500715629101452 0.7183757897842115 NC_006599.3 64289059 32165955 0.5003332682159806 0.7181448003410885 NC_006600.3 55844845 27923160 0.5000132062323747 0.7188366890504118 NC_006601.3 53741614 26870418 0.4999927616613822 0.7159820206379558 NC_006602.3 58134056 29063868 0.4999456428775587 0.7185925003175636 NC_006603.3 50858623 25435529 0.5001222506555083 0.7170182423877624 NC_006604.3 61439934 30709787 0.4998343097178457 0.7177714245114817 NC_006605.3 52294480 26135407 0.4997737237276286 0.7156687320425076 NC_006606.3 47698779 23852652 0.5000683979772312 0.717047003062485 NC_006607.3 51628933 25810141 0.49991621945779896 0.7187175336694263 NC_006608.3 38964690 19494462 0.5003109738586397 0.7174522653026221 NC_006609.3 45876710 22923228 0.49967026842160217 0.7174901186657783 NC_006610.3 41182112 20575923 0.4996325346305697 0.7173775756236732 NC_006611.3 41845238 20902892 0.49952857240291 0.7165020862920836 NC_006612.3 40214260 20099598 0.49981270325501453 0.7177433968387197 NC_006613.3 39895921 19945963 0.49994993222490086 0.7162088849595089 NC_006614.3 38810281 19394095 0.49971539757725536 0.7178494853521302 NC_006615.3 31377067 15693651 0.5001630968248243 0.7169019010675965 NC_006616.3 42124431 21058806 0.4999190612212661 0.7183000172253353 NC_006617.3 26524999 13263538 0.5000391517451142 0.7177062352267785 NC_006618.3 30810995 15406542 0.5000339002359385 0.7176896585513912 NC_006619.3 30902991 15445686 0.4998120084881104 0.7177333037004896 NC_006620.3 23914537 11955086 0.49990873751810455 0.7165081388909298 NC_006621.3 123869142 61897695 0.4997022987371625 0.7179546089186685 NW_003726127.1 2660953 1329948 0.49980138694670667 0.720057874650434 NW_003726128.1 1881673 951207 0.50551131891673 0.7402700017736427 NW_003726129.1 1415205 709177 0.5011125596645009 0.7402837135140817 NW_003726130.1 1067467 538431 0.504400604421495 0.7466079867409431 NW_003726131.1 866315 438829 0.5065466949088957 0.7244430779307132 NW_003726132.1 881102 443899 0.5037997870848097 0.7299344863121917 NW_003726133.1 822601 406451 0.4941046752921526 0.7110155458626862 NW_003726134.1 741967 367165 0.49485354469942733 0.7199698630279106 NW_003726135.1 745551 368916 0.49482329176676043 0.731258595787489 NW_003726136.1 602611 300315 0.4983563194166718 0.7079662150812082 NW_003726137.1 573630 285579 0.4978453009779823 0.7143756002175907 NW_003726138.1 666183 332987 0.4998431361953097 0.7626365149483028 NW_003726139.1 557017 279855 0.5024173409429156 0.7157614750318982 NW_003726140.1 510604 262404 0.5139090175556792 0.7211521322800156 NW_003726141.1 497093 257687 0.5183879072930015 0.7336425534722825 NW_003726142.1 492630 250782 0.5090676572681323 0.742332504250601 NW_003726143.1 577062 283459 0.49121064980885937 0.7394805484010024 NW_003726144.1 561270 277506 0.4944251429793148 0.7520370465313551 NW_003726145.1 407330 204616 0.5023347163233741 0.7200430754080545 NW_003726146.1 405216 203342 0.5018113796098871 0.7257441378888229 NW_003726147.1 508668 256167 0.5036035292174856 0.7637327199704772 NW_003726148.1 540093 269373 0.49875299254017363 0.7861114565754449 NW_003726149.1 448434 222278 0.49567606381318097 0.7470099061086732 NW_003726150.1 377800 187760 0.4969825304393859 0.7208381567639802 NW_003726151.1 384880 192889 0.5011665973810019 0.7348125934628947 NW_003726152.1 367143 181200 0.49354066399195956 0.7159171760214745 NW_003726153.1 399987 202780 0.5069664764104833 0.7451916579623422 NW_003726154.1 376204 190149 0.5054411967974822 0.7377007605141596 NW_003726155.1 416178 207873 0.4994809913066044 0.7471401965184927 NW_003726156.1 365470 183861 0.5030809642378308 0.7471378645227625 NW_003726157.1 322752 159979 0.49567159924648024 0.7201816283743863 NW_003726158.1 320591 161702 0.5043872098717681 0.7468207622098327 NW_003726159.1 310270 155669 0.5017210816385729 0.7163939807109921 NW_003726160.1 433650 216489 0.49922518159806295 0.7909321807422075 NW_003726161.1 273228 135625 0.4963803124130763 0.7096964840952255 NW_003726162.1 281659 140365 0.4983508426856589 0.7339038027422932 NW_003726163.1 320442 161969 0.5054549653291391 0.7360172698038925 NW_003726164.1 265648 133784 0.5036138047340842 0.7334657523034953 NW_003726165.1 241365 122409 0.5071530669318253 0.6956516090616851 NW_003726166.1 234529 116962 0.4987101808305156 0.7225650833933653 NW_003726167.1 252720 127176 0.5032288698955366 0.7552021635726854 NW_003726168.1 254975 127788 0.5011785469163643 0.7163918970110446 NW_003726169.1 226053 113959 0.5041251387948844 0.7163535642783374 NW_003726170.1 223744 114626 0.5123087099542334 0.757024684439276 NW_003726171.1 227140 116677 0.5136787884124329 0.7309871702998917 NW_003726172.1 219672 110983 0.5052214210277141 0.744514697291889 NW_003726173.1 214597 110670 0.5157108440472141 0.7024449214670411 NW_003726174.1 386314 192236 0.4976159290111153 0.8362544740611256 NW_003726175.1 204342 100184 0.4902761057442914 0.7340362797842652 NW_003726176.1 201724 101087 0.5011153853780412 0.7224921734704189 NW_003726177.1 216332 110374 0.5102065344008283 0.7464259136796415 NW_003726178.1 200877 100533 0.5004704371331711 0.726115978196202 NW_003726179.1 310654 152090 0.4895800472551456 0.7921502238760225 NW_003726180.1 200932 100813 0.5017269524018075 0.6966291696161414 NW_003726181.1 201410 99259 0.4928206146666005 0.7093583241844188 NW_003726182.1 292533 142167 0.48598619642912083 0.7945560946502234 NW_003726183.1 192561 95957 0.4983200128790357 0.696894208268244 NW_003726184.1 210134 113095 0.5382041935146145 0.773375854779836 NW_003726185.1 197844 100775 0.5093659651038192 0.7293758020557796 NW_003726186.1 196813 105309 0.5350713621559552 0.7329655443356561 NW_003726187.1 180359 90588 0.5022649271730272 0.7280447720047795 NW_003726188.1 210247 102306 0.48659909534975526 0.7216540504359336 NW_003726189.1 177735 89670 0.504515148957718 0.7051266430359195 NW_003726190.1 172100 87001 0.5055258570598489 0.7137012003548547 NW_003726191.1 166866 83660 0.5013603729938994 0.7116491758971393 NW_003726192.1 164926 81584 0.4946703369996241 0.7417547079758349 NW_003726193.1 157598 79184 0.502442924402594 0.70854893053556 NW_003726194.1 143980 71981 0.49993749131823867 0.7329816394047931 NW_003726195.1 141074 72016 0.5104838595347123 0.7233768084965606 NW_003726196.1 139526 69588 0.4987457534796382 0.7113216768878197 NW_003726197.1 142260 75572 0.5312245184872768 0.7383633108608044 NW_003726198.1 138160 69017 0.49954400694846557 0.7527786703467223 NW_003726199.1 142296 74079 0.5205979085849216 0.7592842831264424 NW_003726200.1 133119 67495 0.5070275467814512 0.7330427111703129 NW_003726201.1 129748 64476 0.49693251533742333 0.7278055672024258 NW_003726202.1 125962 67492 0.5358123878630063 0.719692635509295 NW_003726203.1 127429 63891 0.5013850850277409 0.7325874771299523 NW_003726204.1 128261 64498 0.5028652513234733 0.7128719647293984 NW_003726205.1 131872 65708 0.49827105071584565 0.7493296246275951 NW_003726206.1 133432 70454 0.5280142694406139 0.7824614018008295 NW_003726207.1 119670 57013 0.4764184841647865 0.6884497596091435 NW_003726208.1 144750 68673 0.47442487046632126 0.7542585278620471 NW_003726209.1 120779 59700 0.49429122612374665 0.779514123649373 NW_003726210.1 115952 57601 0.4967659031323306 0.7060356998190955 NW_003726211.1 118237 61488 0.520040258125629 0.7440612210783504 NW_003726212.1 111908 57303 0.512054544804661 0.7146996486489592 NW_003726213.1 117332 59985 0.5112416050182389 0.8051745659271863 NW_003726214.1 111759 55804 0.49932443919505365 0.7305102357160763 NW_003726215.1 108801 57596 0.5293701344656758 0.7467422189310307 NW_003726216.1 112014 59681 0.5327994714946346 0.726672722795922 NW_003726217.1 106428 56983 0.5354136129589957 0.7383059235495724 NW_003726218.1 104912 51279 0.48878107366173557 0.707376397139609 NW_003726219.1 104646 52224 0.4990539533283642 0.7416070876319534 NW_003726220.1 103248 51881 0.5024891523322486 0.7033950488309471 NW_003726221.1 129482 62088 0.4795106655751379 0.753876215579592 NW_003726222.1 118473 62690 0.5291501017109383 0.7705429512948838 NW_003726223.1 99993 48873 0.48876421349494464 0.6792373612473974 NW_003726224.1 109585 52798 0.48179951635716567 0.6843095812568604 NW_003726225.1 124049 62403 0.5030512136333223 0.756153906424621 NW_003726226.1 99658 48600 0.4876678239579361 0.7169553614359117 NW_003726227.1 101741 51905 0.5101679755457486 0.7223371835419191 NW_003726228.1 97365 48600 0.49915267293175164 0.736243408854619 NW_003726229.1 94395 47675 0.5050585306425128 0.7175104915188011 NW_003726230.1 102992 57926 0.5624320335560044 0.8105392592256856 NW_003726231.1 95509 47384 0.49612078442869256 0.732897191142355 NW_003726232.1 92047 45881 0.49845187784501394 0.7564400758390535 NW_003726233.1 87753 43174 0.4919945756840222 0.7111853312378766 NW_003726234.1 96536 52477 0.543600314908428 0.7771695113515991 NW_003726235.1 86544 45017 0.5201631540025883 0.7314444042569043 NW_003726236.1 85476 41694 0.48778604520567176 0.7475293853401119 NW_003726237.1 110512 57314 0.5186224120457507 0.7750527955523849 NW_003726238.1 83291 42278 0.5075938576797013 0.7059399824690982 NW_003726239.1 82459 43515 0.5277168047150705 0.7392513719208123 NW_003726240.1 81605 40195 0.4925556032105876 0.7134208857565894 NW_003726241.1 82380 42587 0.5169579995144452 0.6977958829617088 NW_003726242.1 102198 48879 0.47827746139846183 0.7126972944971645 NW_003726243.1 82108 42017 0.5117284552053393 0.7416779777822379 NW_003726244.1 87041 41690 0.47896968095495224 0.7219963219691173 NW_003726245.1 79722 41700 0.5230676601189133 0.7393175080468589 NW_003726246.1 230124 110366 0.47959361040134885 0.951154927249899 NW_003726247.1 78357 40201 0.5130492489503171 0.6961205418673208 NW_003726248.1 256406 127535 0.4973947567529621 1.0614513814617375 NW_003726249.1 78050 40199 0.5150416399743754 0.7279696632529655 NW_003726250.1 81930 40499 0.4943122177468571 0.7431322247599297 NW_003726251.1 77100 39616 0.5138261997405966 0.7173548618241817 NW_003726252.1 77130 37480 0.4859328406586283 0.7121851380612094 NW_003726253.1 79078 40184 0.5081565037052025 0.6967272617674837 NW_003726254.1 90550 42589 0.4703368304803976 0.7234050686230518 NW_003726255.1 82767 39897 0.4820399434557251 0.7230099579741502 NW_003726256.1 89070 41399 0.46479173683619623 0.720138692748446 NW_003726257.1 97802 48583 0.49674853274984154 0.732074248561352 NW_003726258.1 79712 39884 0.5003512645523887 0.7261530831895254 NW_003726259.1 79581 42910 0.5391990550508288 0.7364386065319013 NW_003726260.1 73720 36605 0.49654096581660334 0.6904009758356572 NW_003726261.1 97799 47095 0.48154889109295596 0.7762161004187262 NW_003726262.1 73171 38089 0.5205477579915541 0.7389638334891491 NW_003726263.1 104732 52812 0.5042584883321239 0.7892284934186498 NW_003726264.1 78935 38708 0.4903781592449484 0.7465183070990529 NW_003726265.1 72992 36591 0.5013015124945199 0.7028308298604106 NW_003726266.1 68721 34194 0.49757715982014233 0.7142446771055324 NW_003726267.1 73611 37186 0.505169064406135 0.7443166658027981 NW_003726268.1 68272 33877 0.49620635106632294 0.716703612746541 NW_003726269.1 79297 41099 0.5182919908697681 0.7939728619380819 NW_003726270.1 84443 39587 0.468801440024632 0.7305230771601106 NW_003726271.1 80679 37215 0.46127245007994644 0.783981512180874 NW_003726272.1 68834 33905 0.49256181538193333 0.7396730773017134 NW_003726273.1 67496 33587 0.49761467346213106 0.7332290894621678 NW_003726274.1 66523 36003 0.5412113103738556 0.7569699500410099 NW_003726275.1 67057 33287 0.4963985862773461 0.7359664813119844 NW_003726276.1 66195 33892 0.5120024171009895 0.6923414763958757 NW_003726277.1 87584 45290 0.5171035805626598 0.8502551738928434 NW_003726278.1 84679 33298 0.39322618358743017 0.6843797276798003 NW_003726279.1 65840 32420 0.49240583232077767 0.7129003121361753 NW_003726280.1 65696 33614 0.511659766195811 0.7166831199588553 NW_003726281.1 66021 33906 0.5135638660426228 0.7920878269104803 NW_003726282.1 67300 34489 0.5124665676077266 0.7073926524227916 NW_003726283.1 88153 41705 0.4730979093167561 0.7478820854446259 NW_003726284.1 92437 45115 0.48806213961941647 0.7860579018281737 NW_003726285.1 70351 33585 0.47739193472729596 0.7346493385366213 NW_003726286.1 64646 31491 0.4871299074962101 0.6972037040466513 NW_003726287.1 69126 32989 0.4772299858229899 0.7599591526025887 NW_003726288.1 227674 103793 0.4558842906963465 1.0056650430320087 NW_003726289.1 64123 30008 0.467975609375731 0.6806744652026263 NW_003726290.1 61944 31199 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1500 0.7503751875937968 0.6945932905119833 NW_003729350.1 1819 901 0.4953271028037383 0.7106744949776067 NW_003729351.1 1790 300 0.16759776536312848 0.3735087072725537 NW_003729352.1 1685 900 0.5341246290801187 0.5709525768412969 NW_003729353.1 1573 1194 0.7590591226954864 0.9957581385573685 NW_003729354.1 1115 299 0.2681614349775785 0.4430021216296197 NC_002008.4 16727 8400 0.5021821007951217 0.6798744794254125