BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_hi_error_no_variance/alignment/1X_hi_error_no_variance.sorted.bam outfile = results/1X_hi_error_no_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 = 16,073,035 (100%) number of supplementary alignments = 294 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,036,517 number of mapped paired reads (second in pair) = 8,036,518 number of mapped paired reads (both in pair) = 16,073,006 number of mapped paired reads (singletons) = 29 number of mapped bases = 2,403,439,762 bp number of sequenced bases = 2,403,417,898 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,691 duplication rate = 0.34% >>>>>>> Insert size mean insert size = 502.666 std insert size = 78,157.3125 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.6373 >>>>>>> ACTG content number of A's = 705,425,916 bp (29.35%) number of C's = 506,563,643 bp (21.08%) number of T's = 695,170,285 bp (28.92%) number of G's = 496,254,098 bp (20.65%) number of N's = 3,956 bp (0%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.049 number of mismatches = 117,695,899 number of insertions = 13,917 mapped reads with insertion percentage = 0.09% number of deletions = 11,121 mapped reads with deletion percentage = 0.07% homopolymer indels = 25.48% >>>>>>> Coverage mean coverageData = 0.9969X std coverageData = 1.0192X There is a 62.28% of reference with a coverageData >= 1X There is a 26.39% of reference with a coverageData >= 2X There is a 8.34% of reference with a coverageData >= 3X There is a 2.11% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.09% 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 122383452 0.9975926318474706 1.01659742107823 NC_006584.3 85426708 85430902 1.0000490947163738 1.0188920958426282 NC_006585.3 91889043 91695016 0.9978884642426845 1.0147828949579445 NC_006586.3 88276631 88061462 0.9975625599033112 1.0168105195353767 NC_006587.3 88915250 88653470 0.9970558481250404 1.015361265639776 NC_006588.3 77573801 77364310 0.9972994619665472 1.016451503272442 NC_006589.3 80974532 80767548 0.9974438382675679 1.015987361336318 NC_006590.3 74330416 74113738 0.9970849349208539 1.017058918141617 NC_006591.3 61074082 61030409 0.9992849176185734 1.0202398295594994 NC_006592.3 69331447 69111209 0.9968234039598222 1.016544951845999 NC_006593.3 74389097 74184855 0.9972544094734743 1.015809964502581 NC_006594.3 72498081 72270690 0.996863489393602 1.0172565020226885 NC_006595.3 63241923 63077379 0.9973981815828086 1.0162534506150591 NC_006596.3 60966679 60805418 0.9973549321917305 1.0172961541025431 NC_006597.3 64190966 63987201 0.9968256436583304 1.0172049611290308 NC_006598.3 59632846 59554314 0.9986830747605103 1.0197392551728175 NC_006599.3 64289059 64143572 0.99773698663096 1.0162233471857811 NC_006600.3 55844845 55688490 0.9972001892027814 1.017468432838682 NC_006601.3 53741614 53581633 0.99702314485754 1.015499910606473 NC_006602.3 58134056 57949153 0.9968193686674812 1.0182898467741721 NC_006603.3 50858623 50708518 0.99704858308885 1.015820964927042 NC_006604.3 61439934 61251579 0.9969343228786671 1.0132021932948732 NC_006605.3 52294480 52104923 0.9963752005947856 1.012406824970596 NC_006606.3 47698779 47569002 0.9972792385314517 1.0156116925846705 NC_006607.3 51628933 51446648 0.9964693246711103 1.0141983081609698 NC_006608.3 38964690 38894342 0.9981945705201299 1.0186897581766243 NC_006609.3 45876710 45720936 0.9966045080390464 1.0183951229172943 NC_006610.3 41182112 41050685 0.9968086386633109 1.017304316850956 NC_006611.3 41845238 41702955 0.9965997803621047 1.0138900995167461 NC_006612.3 40214260 40085292 0.9967929784111407 1.0169971338043426 NC_006613.3 39895921 39755890 0.996490092307933 1.0135506345309668 NC_006614.3 38810281 38677949 0.9965902849299133 1.014148888656491 NC_006615.3 31377067 31283794 0.997027351218009 1.0157106366489481 NC_006616.3 42124431 41979777 0.9965660307672761 1.017029670974694 NC_006617.3 26524999 26438964 0.9967564560511388 1.0147993583456296 NC_006618.3 30810995 30704354 0.9965388654277475 1.0146254847431921 NC_006619.3 30902991 30798264 0.9966111047309304 1.01700499250176 NC_006620.3 23914537 23857678 0.9976224084957196 1.0194586633125393 NC_006621.3 123869142 123533020 0.9972864751093538 1.0185055766296522 NW_003726127.1 2660953 2663167 1.000832032734137 1.0261754112915358 NW_003726128.1 1881673 1887480 1.0030860835012247 1.068657091791086 NW_003726129.1 1415205 1420419 1.0036842718899381 1.0662360095644419 NW_003726130.1 1067467 1068600 1.0010613911249715 1.107512046465849 NW_003726131.1 866315 862549 0.9956528514454904 1.0086857465197336 NW_003726132.1 881102 885542 1.005039144162651 1.0585661760962382 NW_003726133.1 822601 828381 1.0070264927954136 1.0625641212916648 NW_003726134.1 741967 747876 1.0079639660523985 1.0271521492677596 NW_003726135.1 745551 737561 0.9892830939801569 1.11276608778928 NW_003726136.1 602611 608523 1.0098106406952412 1.0313476423132237 NW_003726137.1 573630 570617 0.9947474853128323 1.0490831778748089 NW_003726138.1 666183 659418 0.9898451326437331 1.0967444582720194 NW_003726139.1 557017 559754 1.0049136740889417 1.067313658635553 NW_003726140.1 510604 508189 0.9952703073223085 1.0007444590217647 NW_003726141.1 497093 498497 1.0028244211847683 1.0321014503532286 NW_003726142.1 492630 487359 0.9893002862188661 1.0288645602197821 NW_003726143.1 577062 574888 0.9962326405134977 1.1476115727849499 NW_003726144.1 561270 554758 0.988397740837743 1.1347993312115714 NW_003726145.1 407330 407270 0.9998526992855915 1.012824973911748 NW_003726146.1 405216 412045 1.0168527402669194 1.0354414941877512 NW_003726147.1 508668 505331 0.9934397288604748 1.1354486910471193 NW_003726148.1 540093 538495 0.9970412503031886 1.216670166947048 NW_003726149.1 448434 446381 0.9954218458011659 1.0929360813981628 NW_003726150.1 377800 377568 0.9993859184753838 1.0528112276328905 NW_003726151.1 384880 383088 0.9953440033257119 1.0813278764569894 NW_003726152.1 367143 370667 1.0095984398449651 1.0376682336638892 NW_003726153.1 399987 402009 1.0050551642928396 1.0740469903104635 NW_003726154.1 376204 370541 0.9849469968421388 1.040372389077075 NW_003726155.1 416178 413153 0.9927314754744364 1.1043183475031664 NW_003726156.1 365470 364512 0.9973787178154158 1.0650286045937922 NW_003726157.1 322752 331837 1.0281485474915726 1.041161050207842 NW_003726158.1 320591 321853 1.0039364798138437 1.0189783526748912 NW_003726159.1 310270 311486 1.003919167176975 1.0351359062576464 NW_003726160.1 433650 424365 0.9785887236250432 1.1913887763172433 NW_003726161.1 273228 275958 1.009991655320831 1.0055381268505426 NW_003726162.1 281659 276772 0.9826492318725835 1.0219073189667207 NW_003726163.1 320442 320715 1.0008519482464846 1.1341354623992825 NW_003726164.1 265648 266631 1.003700385472505 1.0162826978987078 NW_003726165.1 241365 250398 1.0374246473183768 1.0298487750212701 NW_003726166.1 234529 233422 0.9952799014194407 1.0071690543021945 NW_003726167.1 252720 262167 1.037381291547958 1.0990117731076499 NW_003726168.1 254975 255845 1.0034120992254143 1.1087402930975627 NW_003726169.1 226053 224705 0.9940367966804246 0.9872533734842178 NW_003726170.1 223744 226913 1.0141635082951945 1.059946118031612 NW_003726171.1 227140 229714 1.011332218015321 1.0178816372694104 NW_003726172.1 219672 219672 1.0 1.0123153672918168 NW_003726173.1 214597 215268 1.003126791148059 1.0109741920575819 NW_003726174.1 386314 386045 0.999303675248632 1.3725861892723028 NW_003726175.1 204342 206115 1.008676630354993 0.9891970185141312 NW_003726176.1 201724 203791 1.0102466736729392 1.0758725968227538 NW_003726177.1 216332 214638 0.9921694432631326 1.0822214284614666 NW_003726178.1 200877 199709 0.9941854965974203 0.9943391935183706 NW_003726179.1 310654 299473 0.9640081891750951 1.230670998707203 NW_003726180.1 200932 199937 0.9950480759659984 1.0214832302812005 NW_003726181.1 201410 196439 0.9753190010426493 1.0329347894673302 NW_003726182.1 292533 281162 0.9611291717515631 1.1847093799883408 NW_003726183.1 192561 194877 1.012027357564616 0.994378685142554 NW_003726184.1 210134 206993 0.9850523951383403 1.0489600452499754 NW_003726185.1 197844 206110 1.0417803926325793 1.1003252090993145 NW_003726186.1 196813 206007 1.0467143938662589 1.0814429350355796 NW_003726187.1 180359 181857 1.00830565705066 1.031158565611864 NW_003726188.1 210247 196474 0.9344913363805429 1.0797547763768784 NW_003726189.1 177735 183060 1.0299603342054182 1.0294546994403797 NW_003726190.1 172100 177528 1.0315398024404416 1.0783865682802103 NW_003726191.1 166866 169801 1.017588963599535 1.028938305421429 NW_003726192.1 164926 167634 1.0164194851024095 1.0255952796460963 NW_003726193.1 157598 155300 0.985418596682699 1.0806259885552532 NW_003726194.1 143980 143614 0.9974579802750382 1.0090782681473622 NW_003726195.1 141074 138832 0.9841076314558317 1.028963387620417 NW_003726196.1 139526 141578 1.0147069363416137 1.013147134263633 NW_003726197.1 142260 143150 1.0062561507099677 1.0453058696912298 NW_003726198.1 138160 141767 1.0261074116965836 1.0398645538513769 NW_003726199.1 142296 146809 1.0317155787935008 1.0781993133233676 NW_003726200.1 133119 132348 0.9942081896648863 1.0375159686329631 NW_003726201.1 129748 129362 0.9970250023121744 1.0167799084106863 NW_003726202.1 125962 129142 1.0252457090233562 1.025212556184486 NW_003726203.1 127429 126535 0.9929843285280431 1.0040985933934359 NW_003726204.1 128261 124292 0.9690552857064891 0.9936531367844931 NW_003726205.1 131872 131453 0.9968226765348216 1.0599724196574993 NW_003726206.1 133432 137538 1.0307722285508722 1.089948740955703 NW_003726207.1 119670 125470 1.0484666165287875 1.0714629341892865 NW_003726208.1 144750 142901 0.9872262521588946 1.108922063236829 NW_003726209.1 120779 116323 0.9631061691188038 1.0038197504906394 NW_003726210.1 115952 114198 0.9848730509176211 1.0509703446850056 NW_003726211.1 118237 108356 0.9164305589620846 0.9431753972322073 NW_003726212.1 111908 112427 1.0046377381420453 1.0213023653206668 NW_003726213.1 117332 117442 1.00093751065353 1.042286387655823 NW_003726214.1 111759 111544 0.9980762175753183 1.002192420058296 NW_003726215.1 108801 114468 1.0520859183279565 1.0346650794639696 NW_003726216.1 112014 111313 0.9937418536968593 1.0710495431799538 NW_003726217.1 106428 105552 0.9917690833239373 1.021496120397598 NW_003726218.1 104912 104592 0.9969498246149153 0.9916775843840977 NW_003726219.1 104646 103417 0.9882556428339354 0.9897923257882276 NW_003726220.1 103248 99574 0.9644157756082442 1.0268613758498057 NW_003726221.1 129482 126491 0.976900264129377 1.141693939839058 NW_003726222.1 118473 119681 1.0101964160610435 1.115125231259866 NW_003726223.1 99993 104287 1.0429430060104208 1.0507298937660374 NW_003726224.1 109585 111265 1.0153305653145959 1.0149866851264144 NW_003726225.1 124049 112493 0.9068432635490814 1.0815765083154845 NW_003726226.1 99658 96712 0.9704389010415622 1.0437023454551069 NW_003726227.1 101741 101477 0.9974051758877935 1.0368682331683334 NW_003726228.1 97365 99097 1.01778873311765 1.0600962872227873 NW_003726229.1 94395 93984 0.9956459558239313 1.018974653063783 NW_003726230.1 102992 101735 0.9877951685567811 1.068892897824806 NW_003726231.1 95509 92318 0.966589536064664 1.0798966967159558 NW_003726232.1 92047 90201 0.979945028083479 1.0108592567996857 NW_003726233.1 87753 86086 0.9810034984558933 0.9937260186228608 NW_003726234.1 96536 101361 1.0499813541062402 1.0965917499831728 NW_003726235.1 86544 88038 1.017262895174709 1.0241029494241476 NW_003726236.1 85476 85555 1.0009242360428658 0.964536399966491 NW_003726237.1 110512 112488 1.0178804111770667 1.1953817337592636 NW_003726238.1 83291 83502 1.00253328690975 1.0416433056818877 NW_003726239.1 82459 85469 1.0365029893644113 0.9799868049300806 NW_003726240.1 81605 86665 1.0620060045340358 0.9844962597434809 NW_003726241.1 82380 83276 1.0108764263170673 1.051388143103375 NW_003726242.1 102198 99069 0.9693829624845888 1.172983346934934 NW_003726243.1 82108 80142 0.9760559263409169 1.0756957863844028 NW_003726244.1 87041 82912 0.952562585448237 1.0297954896095138 NW_003726245.1 79722 79287 0.9945435387973207 1.0259339200998474 NW_003726246.1 230124 224599 0.9759912047417914 1.7125326885464625 NW_003726247.1 78357 77558 0.9898030807713414 1.0371363740170478 NW_003726248.1 256406 252625 0.9852538552139966 1.8129436836535635 NW_003726249.1 78050 78578 1.0067648942985266 0.9739096673598341 NW_003726250.1 81930 83593 1.0202978152081046 1.1085163779120923 NW_003726251.1 77100 80378 1.0425162127107652 1.0310272908029487 NW_003726252.1 77130 78052 1.0119538441592117 0.9718785353153877 NW_003726253.1 79078 79625 1.0069172209716988 1.001088396508645 NW_003726254.1 90550 85276 0.9417559359469906 1.0956911784550785 NW_003726255.1 82767 85467 1.0326216970531734 1.1410060182247919 NW_003726256.1 89070 89189 1.0013360278432692 1.1339838625897523 NW_003726257.1 97802 95247 0.9738757898611481 1.1452740509221635 NW_003726258.1 79712 79468 0.996938980329185 1.0316842562268607 NW_003726259.1 79581 77470 0.9734735678114123 1.0290199718473165 NW_003726260.1 73720 72602 0.9848345089527943 0.9956569074946431 NW_003726261.1 97799 94450 0.965756296076647 1.0918245639713362 NW_003726262.1 73171 75057 1.0257752388241244 1.003821999433169 NW_003726263.1 104732 104574 0.9984913875415345 1.2101248080238443 NW_003726264.1 78935 72169 0.9142839044783683 1.009353422771052 NW_003726265.1 72992 71729 0.9826967338886453 1.07228053129641 NW_003726266.1 68721 72510 1.0551359846335182 1.0487740905191527 NW_003726267.1 73611 73532 0.9989267908328918 1.0521053723830545 NW_003726268.1 68272 67635 0.9906696742441997 1.0133068281655833 NW_003726269.1 79297 77784 0.9809198330327755 1.1146160610766178 NW_003726270.1 84443 84276 0.9980223345925654 1.1074228825364423 NW_003726271.1 80679 81722 1.012927775505398 1.090800524578328 NW_003726272.1 68834 65737 0.955007699683296 1.0224380627441714 NW_003726273.1 67496 67296 0.9970368614436411 1.1272154470917055 NW_003726274.1 66523 66197 0.9950994392916735 0.9952641222099596 NW_003726275.1 67057 67320 1.0039220364764305 1.020905074129571 NW_003726276.1 66195 65988 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