BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_hi_error_med_variance/alignment/1X_hi_error_med_variance.sorted.bam outfile = results/1X_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 = 16,073,088 number of mapped reads = 16,072,930 (100%) number of supplementary alignments = 546 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,036,458 number of mapped paired reads (second in pair) = 8,036,472 number of mapped paired reads (both in pair) = 16,072,840 number of mapped paired reads (singletons) = 90 number of mapped bases = 2,399,377,304 bp number of sequenced bases = 2,397,788,285 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,128 duplication rate = 0.34% >>>>>>> Insert size mean insert size = 542.5336 std insert size = 84,030.6612 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.3122 >>>>>>> ACTG content number of A's = 702,970,225 bp (29.32%) number of C's = 506,116,647 bp (21.11%) number of T's = 692,819,554 bp (28.89%) number of G's = 495,878,056 bp (20.68%) number of N's = 3,803 bp (0%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0551 number of mismatches = 130,744,881 number of insertions = 1,105,709 mapped reads with insertion percentage = 6.66% number of deletions = 1,109,705 mapped reads with deletion percentage = 6.68% homopolymer indels = 27.57% >>>>>>> Coverage mean coverageData = 0.9952X std coverageData = 1.018X There is a 62.19% of reference with a coverageData >= 1X There is a 26.31% of reference with a coverageData >= 2X There is a 8.31% 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 0.02% 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 122166753 0.9958262384160391 1.0152232756510928 NC_006584.3 85426708 85276611 0.9982429733801752 1.017333185628575 NC_006585.3 91889043 91518309 0.9959654166819433 1.0144603917068507 NC_006586.3 88276631 87903297 0.9957708626193494 1.0149343538809859 NC_006587.3 88915250 88509232 0.9954336517076654 1.015705028016733 NC_006588.3 77573801 77221130 0.9954537357270917 1.016756195848905 NC_006589.3 80974532 80629652 0.9957408830717293 1.016669117034217 NC_006590.3 74330416 74048164 0.9962027388626481 1.015121607439469 NC_006591.3 61074082 60903504 0.9972070312902943 1.0175989625183124 NC_006592.3 69331447 69014512 0.9954286977451949 1.0149497562057113 NC_006593.3 74389097 74075761 0.995787877355199 1.0153507620075661 NC_006594.3 72498081 72142143 0.9950903803922755 1.0160459409291371 NC_006595.3 63241923 62936034 0.995163192618289 1.0158765545229531 NC_006596.3 60966679 60695275 0.9955483223877095 1.014162209594642 NC_006597.3 64190966 63872285 0.9950354228973591 1.0147464778650856 NC_006598.3 59632846 59424520 0.996506522596624 1.0146585202675835 NC_006599.3 64289059 64013019 0.9957062678425578 1.0161153454867689 NC_006600.3 55844845 55601173 0.9956366250098823 1.016750847181683 NC_006601.3 53741614 53485327 0.9952311257343331 1.0167580823878528 NC_006602.3 58134056 57854431 0.995189996720683 1.0154914681717286 NC_006603.3 50858623 50632492 0.9955537333364295 1.0162916398365185 NC_006604.3 61439934 61123837 0.9948551865306365 1.0131051967071123 NC_006605.3 52294480 52045928 0.9952470700540478 1.0157645298981843 NC_006606.3 47698779 47504568 0.9959283863429712 1.01713480971416 NC_006607.3 51628933 51361844 0.9948267573145468 1.0157360776670252 NC_006608.3 38964690 38808333 0.9959872130382662 1.016834743775152 NC_006609.3 45876710 45663327 0.9953487728304842 1.0149031254876748 NC_006610.3 41182112 40970941 0.9948722639577106 1.0142512907403365 NC_006611.3 41845238 41629546 0.9948454827763197 1.0118609943882215 NC_006612.3 40214260 40015487 0.9950571513686935 1.0133259197160096 NC_006613.3 39895921 39716693 0.9955076109159129 1.0147293040349912 NC_006614.3 38810281 38611591 0.994880480252127 1.0084101343568996 NC_006615.3 31377067 31222760 0.9950821725943984 1.0117891055104453 NC_006616.3 42124431 41915880 0.9950491675483997 1.0158243305184935 NC_006617.3 26524999 26382545 0.9946294437183579 1.01394840879488 NC_006618.3 30810995 30655745 0.9949612143327407 1.0132959159077446 NC_006619.3 30902991 30750252 0.9950574687090968 1.0163940239014362 NC_006620.3 23914537 23808996 0.995586742908717 1.0136587015666163 NC_006621.3 123869142 123323349 0.9955937936503992 1.0166148251317768 NW_003726127.1 2660953 2657107 0.9985546531637349 1.0318189276878647 NW_003726128.1 1881673 1882148 1.0002524349342314 1.0713362462584317 NW_003726129.1 1415205 1412797 0.9982984797255521 1.065319662532871 NW_003726130.1 1067467 1066134 0.9987512494531446 1.0914146273379832 NW_003726131.1 866315 863472 0.9967182837651432 1.0128069765525307 NW_003726132.1 881102 874438 0.9924367439865078 1.0437446416098195 NW_003726133.1 822601 820799 0.9978093875402534 1.0441083480620774 NW_003726134.1 741967 738408 0.9952032907123902 1.0171111538343864 NW_003726135.1 745551 743998 0.997916976839948 1.1183236696428347 NW_003726136.1 602611 605764 1.005232231074441 1.0180274175999653 NW_003726137.1 573630 566592 0.9877307672192877 1.012629123905242 NW_003726138.1 666183 651986 0.9786890388977203 1.1166665777490745 NW_003726139.1 557017 560519 1.0062870612566583 1.0689410168112166 NW_003726140.1 510604 517516 1.0135369092290698 1.0421205690731674 NW_003726141.1 497093 492122 0.98999985918128 1.0388665464282474 NW_003726142.1 492630 483082 0.9806183139475875 1.0304049041940004 NW_003726143.1 577062 573464 0.9937649680623573 1.137601379324583 NW_003726144.1 561270 557970 0.9941204767758832 1.1214690716449154 NW_003726145.1 407330 404319 0.9926079591486019 1.009087401817437 NW_003726146.1 405216 408385 1.007820520413804 1.0390466961785692 NW_003726147.1 508668 506071 0.9948945087955209 1.1433003140899651 NW_003726148.1 540093 536300 0.9929771354192704 1.2056242639416583 NW_003726149.1 448434 453055 1.0103047494168595 1.1715563118909291 NW_003726150.1 377800 378885 1.00287188988883 1.063129692008428 NW_003726151.1 384880 381883 0.9922131573477447 1.0489008977806864 NW_003726152.1 367143 369751 1.0071034991815178 1.0367464635737038 NW_003726153.1 399987 396018 0.9900771775082691 1.0782229906356016 NW_003726154.1 376204 374470 0.9953907986092652 1.0450531226605082 NW_003726155.1 416178 405380 0.9740543709662692 1.1172503991360532 NW_003726156.1 365470 367775 1.0063069472186499 1.1043226808683033 NW_003726157.1 322752 327544 1.0148473131072775 1.0260255953297024 NW_003726158.1 320591 323933 1.0104244972566292 1.0352268669917442 NW_003726159.1 310270 309016 0.9959583588487446 1.0273191291549655 NW_003726160.1 433650 436470 1.0065029401591146 1.2253920989660383 NW_003726161.1 273228 276009 1.0101783126180333 1.0183216740168735 NW_003726162.1 281659 284829 1.0112547442119726 1.0402030100078192 NW_003726163.1 320442 329656 1.0287540334912402 1.1367897126776032 NW_003726164.1 265648 261369 0.9838922182738059 0.9949247871687635 NW_003726165.1 241365 253639 1.0508524433948585 1.0887869263931893 NW_003726166.1 234529 233068 0.9937704932012672 0.9949937762420239 NW_003726167.1 252720 251871 0.9966405508072175 1.0971055559295693 NW_003726168.1 254975 257633 1.0104245514266104 1.079276223142836 NW_003726169.1 226053 226244 1.0008449345949844 1.0302758009324682 NW_003726170.1 223744 228186 1.0198530463386728 1.0348391818982503 NW_003726171.1 227140 226987 0.999326406621467 1.0325185994514643 NW_003726172.1 219672 217170 0.9886102917076368 1.0077904971488747 NW_003726173.1 214597 213832 0.9964351784973695 1.0166492715673847 NW_003726174.1 386314 381062 0.9864048416573047 1.396727069394313 NW_003726175.1 204342 209945 1.0274197179238727 1.0320292188425841 NW_003726176.1 201724 208942 1.0357815629275644 1.038578075870239 NW_003726177.1 216332 217986 1.0076456557513451 1.0834774924732775 NW_003726178.1 200877 202424 1.0077012301059853 0.9993257192322473 NW_003726179.1 310654 307628 0.9902592594977049 1.2519649478367902 NW_003726180.1 200932 198908 0.9899269404574682 1.0323848377081248 NW_003726181.1 201410 203202 1.0088972742167717 1.0263995060784274 NW_003726182.1 292533 279196 0.9544085624527832 1.1793584712844873 NW_003726183.1 192561 191291 0.9934046873458281 0.9948569643626674 NW_003726184.1 210134 215784 1.0268876050520144 1.093083830954731 NW_003726185.1 197844 198278 1.0021936475202684 1.0726895409599244 NW_003726186.1 196813 201413 1.0233724398286699 1.0996438249320197 NW_003726187.1 180359 181983 1.0090042637184726 1.0482377016339492 NW_003726188.1 210247 200735 0.9547579751435217 1.065883354926007 NW_003726189.1 177735 185669 1.0446394913776127 1.0548563572934058 NW_003726190.1 172100 174189 1.0121382916908774 1.0296704259026699 NW_003726191.1 166866 165666 0.9928086009133077 0.9856017708888882 NW_003726192.1 164926 169253 1.0262360088767084 0.9980149536758203 NW_003726193.1 157598 160490 1.0183504866813031 1.1088074383827784 NW_003726194.1 143980 143402 0.995985553549104 1.0301766491336528 NW_003726195.1 141074 139716 0.9903738463501425 1.0350187273096345 NW_003726196.1 139526 137076 0.9824405487149348 0.9769203134067037 NW_003726197.1 142260 138838 0.9759454519893154 1.0424538052880836 NW_003726198.1 138160 139460 1.0094093804284887 0.9937556684181234 NW_003726199.1 142296 141831 0.9967321639399561 1.031885258780698 NW_003726200.1 133119 132971 0.9988882128020793 1.0069308192900923 NW_003726201.1 129748 129125 0.995198384560841 1.0771781795974547 NW_003726202.1 125962 134856 1.0706085962433114 1.0617633347456044 NW_003726203.1 127429 127177 0.99802242817569 1.0330076952068497 NW_003726204.1 128261 125955 0.9820210352328456 1.0086084890429818 NW_003726205.1 131872 134019 1.0162809390924532 1.0700697695421795 NW_003726206.1 133432 132676 0.994334192697404 1.1198012700499074 NW_003726207.1 119670 121530 1.0155427425419905 1.0101014338989336 NW_003726208.1 144750 143320 0.9901208981001727 1.1300591948279637 NW_003726209.1 120779 120982 1.0016807557605212 1.029270172955085 NW_003726210.1 115952 112442 0.9697288533186146 0.9936016071380317 NW_003726211.1 118237 111347 0.9417272089109162 1.0028486625002166 NW_003726212.1 111908 110314 0.9857561568431211 1.0169089989033944 NW_003726213.1 117332 118917 1.0135086762349572 1.0418937601787754 NW_003726214.1 111759 111334 0.996197174276792 1.030897521907825 NW_003726215.1 108801 109907 1.0101653477449655 1.0443113791803496 NW_003726216.1 112014 116265 1.0379506133161926 1.0727785689129246 NW_003726217.1 106428 107990 1.0146765888675913 1.041312193291215 NW_003726218.1 104912 109612 1.0447994509684306 1.0559311524909112 NW_003726219.1 104646 102584 0.9802954723544139 1.0006654513942066 NW_003726220.1 103248 100991 0.9781400123973346 1.0758862425417757 NW_003726221.1 129482 125329 0.9679260437744243 1.141343402131903 NW_003726222.1 118473 118179 0.9975184219189183 1.1178024479734125 NW_003726223.1 99993 102382 1.0238916724170692 1.034301672652174 NW_003726224.1 109585 107683 0.9826436099831182 1.0631628361513734 NW_003726225.1 124049 117929 0.9506646567082363 1.1284329916403597 NW_003726226.1 99658 95822 0.9615083585863654 1.049609644813564 NW_003726227.1 101741 101226 0.9949381272053548 1.048347929940767 NW_003726228.1 97365 101030 1.037641863092487 1.0758330501656383 NW_003726229.1 94395 93221 0.9875629005773611 1.0021411351305167 NW_003726230.1 102992 94235 0.9149739785614417 0.9975826831280371 NW_003726231.1 95509 92061 0.963898690175795 1.0312656925852894 NW_003726232.1 92047 90790 0.9863439329907547 0.9834812480096142 NW_003726233.1 87753 93705 1.0678267409661208 1.0406737151744665 NW_003726234.1 96536 97275 1.0076551752714014 1.1093707294010724 NW_003726235.1 86544 88074 1.0176788685524127 1.0215418123610858 NW_003726236.1 85476 84832 0.992465721372081 0.9794768570958982 NW_003726237.1 110512 112287 1.0160616041696828 1.2020215311316056 NW_003726238.1 83291 83020 0.9967463471443493 1.0692527544557515 NW_003726239.1 82459 83756 1.015729028971974 1.0547278367327702 NW_003726240.1 81605 85628 1.0492984498498867 1.0648145183508455 NW_003726241.1 82380 83506 1.0136683661082788 0.9739942341019853 NW_003726242.1 102198 97211 0.9512025675649229 1.1514915101563583 NW_003726243.1 82108 81124 0.9880157840892483 1.0269739575397157 NW_003726244.1 87041 83495 0.9592605783481348 1.0727348225151965 NW_003726245.1 79722 81115 1.0174732194375455 1.0732372229221632 NW_003726246.1 230124 223668 0.9719455597851593 1.7091232535777143 NW_003726247.1 78357 77817 0.993108465102033 1.0556640304025964 NW_003726248.1 256406 247812 0.966482843615204 1.8143433817016952 NW_003726249.1 78050 74944 0.9602049967969251 0.9799395603594179 NW_003726250.1 81930 79057 0.9649334797998291 1.0226418659272227 NW_003726251.1 77100 76493 0.9921271076523995 1.059570495674747 NW_003726252.1 77130 77637 1.0065733177751848 1.0762409366377501 NW_003726253.1 79078 82402 1.0420344470016945 1.055315736670871 NW_003726254.1 90550 90688 1.0015240198785202 1.156423868721728 NW_003726255.1 82767 80482 0.9723923786049996 1.0424505994015694 NW_003726256.1 89070 77934 0.87497473896935 1.0005792448975828 NW_003726257.1 97802 97685 0.9988037054456964 1.132374315336774 NW_003726258.1 79712 79363 0.9956217382577278 1.038010562902388 NW_003726259.1 79581 79897 1.003970797049547 1.1054817841522824 NW_003726260.1 73720 74087 1.0049782962561042 1.0566864620325949 NW_003726261.1 97799 98314 1.0052659025143407 1.2207076259152043 NW_003726262.1 73171 70756 0.9669951210178896 0.973843038863713 NW_003726263.1 104732 97116 0.9272810602299202 1.171563879532966 NW_003726264.1 78935 75549 0.957103946284918 1.0922227477955264 NW_003726265.1 72992 74981 1.0272495615957913 1.0446438095698956 NW_003726266.1 68721 70167 1.0210416030034488 0.9817238747167648 NW_003726267.1 73611 67082 0.9113040170626673 1.014324824469376 NW_003726268.1 68272 68023 0.9963528239981252 1.0291968327348635 NW_003726269.1 79297 78883 0.9947791215304488 1.1298441460200888 NW_003726270.1 84443 87048 1.030849211894414 1.1651717424429948 NW_003726271.1 80679 74852 0.9277755053979351 1.0591912422452678 NW_003726272.1 68834 68023 0.988218031786617 1.0118241555619556 NW_003726273.1 67496 66895 0.9910957686381415 1.017589785482117 NW_003726274.1 66523 69341 1.0423612885768831 1.0345151680142597 NW_003726275.1 67057 66909 0.997792922439119 0.9778441701478958 NW_003726276.1 66195 67208 1.0153032706397764 1.0136903723662445 NW_003726277.1 87584 76149 0.8694396236755572 1.1399662120584468 NW_003726278.1 84679 76201 0.8998807260359711 1.0622828255629444 NW_003726279.1 65840 63285 0.9611938031591738 0.9115883435716511 NW_003726280.1 65696 64489 0.9816274963468096 1.0225595186089147 NW_003726281.1 66021 66379 1.0054225170778994 1.0279231359060892 NW_003726282.1 67300 68833 1.022778603268945 1.101845011929847 NW_003726283.1 88153 78354 0.8888409923655463 1.1827726787857098 NW_003726284.1 92437 82255 0.8898493027683719 1.1487761355566317 NW_003726285.1 70351 71242 1.012665065173203 1.0915667151274977 NW_003726286.1 64646 65838 1.0184388825294681 1.0209983434298058 NW_003726287.1 69126 68411 0.9896565691635564 1.049564993166561 NW_003726288.1 227674 195987 0.8608229310329681 1.7149315122728224 NW_003726289.1 64123 65000 1.0136768398234643 1.0763820409530482 NW_003726290.1 61944 60059 0.9695692883895131 1.013503880346307 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