BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_haploid_hi_error_med_variance/alignment/1X_haploid_hi_error_med_variance.sorted.bam outfile = results/1X_haploid_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 = 16,072,797 (100%) number of supplementary alignments = 720 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,036,401 number of mapped paired reads (second in pair) = 8,036,396 number of mapped paired reads (both in pair) = 16,072,656 number of mapped paired reads (singletons) = 141 number of mapped bases = 2,396,870,397 bp number of sequenced bases = 2,394,506,926 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,511 duplication rate = 0.35% >>>>>>> Insert size mean insert size = 656.7377 std insert size = 119,300.2398 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.1727 >>>>>>> ACTG content number of A's = 701,720,389 bp (29.31%) number of C's = 505,723,856 bp (21.12%) number of T's = 691,547,930 bp (28.88%) number of G's = 495,510,761 bp (20.69%) number of N's = 3,990 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0582 number of mismatches = 137,144,664 number of insertions = 1,641,940 mapped reads with insertion percentage = 9.74% number of deletions = 1,652,278 mapped reads with deletion percentage = 9.79% homopolymer indels = 27.57% >>>>>>> Coverage mean coverageData = 0.9941X std coverageData = 1.0172X There is a 62.14% of reference with a coverageData >= 1X There is a 26.27% of reference with a coverageData >= 2X There is a 8.27% of reference with a coverageData >= 3X There is a 2.09% of reference with a coverageData >= 4X There is a 0.44% 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 122037201 0.9947702123068793 1.0134816304077705 NC_006584.3 85426708 85173405 0.9970348500377657 1.015551947456718 NC_006585.3 91889043 91407234 0.9947566218531626 1.0137553528707324 NC_006586.3 88276631 87817784 0.9948021691040747 1.0140691834101176 NC_006587.3 88915250 88412441 0.9943450757884614 1.0135160485889778 NC_006588.3 77573801 77155630 0.9946093784936489 1.0164524793104532 NC_006589.3 80974532 80554244 0.9948096273035576 1.015309701883404 NC_006590.3 74330416 73921423 0.9944976360686586 1.01544627955851 NC_006591.3 61074082 60863961 0.99655957170179 1.0185669801833581 NC_006592.3 69331447 68941901 0.9943813952130554 1.0160242384165263 NC_006593.3 74389097 73979596 0.9944951475886311 1.0116462096888712 NC_006594.3 72498081 72074673 0.9941597350694014 1.0154626034877698 NC_006595.3 63241923 62869546 0.9941118646882385 1.0122729149826268 NC_006596.3 60966679 60640551 0.9946507173205219 1.0150550184384242 NC_006597.3 64190966 63828762 0.9943573991393119 1.014086246559275 NC_006598.3 59632846 59368742 0.9955711655955511 1.0155821472578936 NC_006599.3 64289059 63931129 0.9944324896713763 1.0133536896277182 NC_006600.3 55844845 55542884 0.994592858123252 1.0174334019931917 NC_006601.3 53741614 53429832 0.9941984995091513 1.0132310805388156 NC_006602.3 58134056 57804766 0.9943356782124406 1.015801479458433 NC_006603.3 50858623 50577639 0.994475194501432 1.0162609831222604 NC_006604.3 61439934 61093817 0.9943665792349321 1.0145130075687825 NC_006605.3 52294480 51977930 0.9939467798513342 1.0135005866970987 NC_006606.3 47698779 47436696 0.9945054568377946 1.0150269990092915 NC_006607.3 51628933 51324099 0.9940956749968085 1.0153439637050328 NC_006608.3 38964690 38766496 0.9949134973228325 1.0136528438421681 NC_006609.3 45876710 45602893 0.9940314595357862 1.0135328007309372 NC_006610.3 41182112 40962663 0.9946712543543177 1.0157384130858602 NC_006611.3 41845238 41577404 0.9935994150636687 1.0139408935417336 NC_006612.3 40214260 39972707 0.9939933496227458 1.0115395093987618 NC_006613.3 39895921 39657827 0.9940321217299383 1.010862498853115 NC_006614.3 38810281 38570521 0.9938222554997733 1.01124521644457 NC_006615.3 31377067 31214245 0.994810796050504 1.0146070634809419 NC_006616.3 42124431 41859016 0.9936992620743055 1.012849947681618 NC_006617.3 26524999 26360813 0.9938101411427009 1.0117546534494932 NC_006618.3 30810995 30632088 0.994193404010484 1.0120932970849794 NC_006619.3 30902991 30722900 0.9941723763890686 1.0123458849679903 NC_006620.3 23914537 23783124 0.9945048904772859 1.0178705751739405 NC_006621.3 123869142 123114878 0.9939107998342315 1.017003306775795 NW_003726127.1 2660953 2658821 0.9991987832930532 1.045600363383936 NW_003726128.1 1881673 1871174 0.9944203907905359 1.074990887096948 NW_003726129.1 1415205 1415615 1.0002897106779582 1.0592278907222323 NW_003726130.1 1067467 1070396 1.0027438787334877 1.0902766178432008 NW_003726131.1 866315 869204 1.0033348147036587 1.0224058486995868 NW_003726132.1 881102 891977 1.0123424983713576 1.053204029144281 NW_003726133.1 822601 828842 1.0075869103003765 1.0502444292393138 NW_003726134.1 741967 744095 1.002868052083179 0.9873970047162677 NW_003726135.1 745551 737645 0.9893957623288011 1.1083838872612268 NW_003726136.1 602611 602508 0.9998290771326777 1.0414810573116124 NW_003726137.1 573630 574268 1.0011122151909768 1.0161874430373548 NW_003726138.1 666183 648479 0.9734247196340945 1.0965002556611085 NW_003726139.1 557017 555585 0.997429162844222 1.0568306746213831 NW_003726140.1 510604 503971 0.9870095024715827 0.9775309349733914 NW_003726141.1 497093 499916 1.0056790178095447 1.0270750388685101 NW_003726142.1 492630 488878 0.992383736272659 1.044336752324505 NW_003726143.1 577062 582118 1.0087616235343861 1.1640628862200766 NW_003726144.1 561270 551708 0.9829636360396957 1.1154017723232885 NW_003726145.1 407330 407987 1.0016129428227727 1.028204671360995 NW_003726146.1 405216 407186 1.0048616046750376 1.0392329548248291 NW_003726147.1 508668 498140 0.9793028065457233 1.12902456823967 NW_003726148.1 540093 532914 0.9867078447600691 1.208353080059004 NW_003726149.1 448434 443942 0.9899829183335787 1.098138728278246 NW_003726150.1 377800 379252 1.003843303335098 1.0423388499938362 NW_003726151.1 384880 383338 0.995993556433174 1.034653397539409 NW_003726152.1 367143 363043 0.9888326891701599 1.0491800667015274 NW_003726153.1 399987 403383 1.0084902759339678 1.112393410636825 NW_003726154.1 376204 374095 0.9943939990005423 1.068099143184029 NW_003726155.1 416178 410748 0.9869526981243603 1.0900580404021998 NW_003726156.1 365470 367826 1.0064464935562427 1.0844641793725969 NW_003726157.1 322752 319737 0.9906584622248662 1.0079544386901862 NW_003726158.1 320591 321258 1.0020805325165085 1.0494913531156682 NW_003726159.1 310270 309988 0.999091114190866 1.0201395264953244 NW_003726160.1 433650 413194 0.9528283177677851 1.18606917062167 NW_003726161.1 273228 275028 1.0065879046071413 1.0176205961149638 NW_003726162.1 281659 276491 0.9816515715812383 1.0432648525107464 NW_003726163.1 320442 321933 1.0046529481154156 1.1170252193087065 NW_003726164.1 265648 269275 1.0136534060109619 1.0059076620741276 NW_003726165.1 241365 242700 1.0055310421975017 1.028597982717202 NW_003726166.1 234529 235601 1.0045708633047512 1.003271879160187 NW_003726167.1 252720 261919 1.0363999683444127 1.0792238600286572 NW_003726168.1 254975 251343 0.9857554662221787 1.1002923576329975 NW_003726169.1 226053 223646 0.9893520546066631 0.9883837051184781 NW_003726170.1 223744 227432 1.016483123569794 1.0235349533890026 NW_003726171.1 227140 227508 1.0016201461653607 1.0281376698422695 NW_003726172.1 219672 213779 0.973173640700681 0.9964988959842945 NW_003726173.1 214597 215576 1.0045620395438892 0.9971727496531582 NW_003726174.1 386314 380741 0.9855739113777912 1.3646005847941214 NW_003726175.1 204342 204532 1.0009298137436258 1.029970718954396 NW_003726176.1 201724 204011 1.0113372727092462 1.0423759205443806 NW_003726177.1 216332 217407 1.0049692139859105 1.0448807168857837 NW_003726178.1 200877 203325 1.0121865619259547 0.9979547753791655 NW_003726179.1 310654 301003 0.9689332826874916 1.2682017106652919 NW_003726180.1 200932 198155 0.9861794039774651 1.0063433152962313 NW_003726181.1 201410 205660 1.0211012362841965 1.0428648150329705 NW_003726182.1 292533 281629 0.9627255728413546 1.2117761513702254 NW_003726183.1 192561 189268 0.9828989255352849 1.0442817235687416 NW_003726184.1 210134 216350 1.0295811244253668 1.0693808520206052 NW_003726185.1 197844 196592 0.9936717818078891 1.080405373872319 NW_003726186.1 196813 204597 1.0395502329622535 1.0516695306424866 NW_003726187.1 180359 182202 1.010218508641099 1.0446822643741114 NW_003726188.1 210247 194442 0.9248265135768882 1.0679097064819574 NW_003726189.1 177735 187333 1.0540017441696907 1.061321067088416 NW_003726190.1 172100 174692 1.015061011040093 1.0048603333707893 NW_003726191.1 166866 172836 1.0357772104562943 1.046914312920474 NW_003726192.1 164926 169328 1.0266907582794709 1.0093009196530844 NW_003726193.1 157598 159460 1.0118148707470906 1.0586885865702103 NW_003726194.1 143980 142887 0.9924086678705376 1.0308949534169158 NW_003726195.1 141074 139558 0.9892538667649602 1.0221017307860178 NW_003726196.1 139526 138150 0.9901380387884695 1.0084162398794998 NW_003726197.1 142260 146878 1.03246168986363 1.0550805088178377 NW_003726198.1 138160 138482 1.0023306311522873 0.9786951108911904 NW_003726199.1 142296 143132 1.0058750773036487 1.0450483870058596 NW_003726200.1 133119 132763 0.9973257010644612 1.0472773265975803 NW_003726201.1 129748 127006 0.9788667262693838 1.0142052559135755 NW_003726202.1 125962 138152 1.0967752179228656 1.067217156647228 NW_003726203.1 127429 128855 1.0111905453232781 0.9966217843155815 NW_003726204.1 128261 124182 0.9681976594600074 1.0274947314310607 NW_003726205.1 131872 133421 1.0117462387769958 1.055085283450945 NW_003726206.1 133432 138813 1.0403276575334253 1.1540718589504841 NW_003726207.1 119670 124291 1.0386145232723323 1.0338504988908541 NW_003726208.1 144750 142558 0.9848566493955095 1.0739475826255531 NW_003726209.1 120779 119483 0.9892696578047508 1.030337782363757 NW_003726210.1 115952 117317 1.0117721125983166 1.0005810196203404 NW_003726211.1 118237 117466 0.9934791985588267 1.0223979595843364 NW_003726212.1 111908 115135 1.0288361868677842 1.0015921647015629 NW_003726213.1 117332 120462 1.0266764395049943 1.0793668902783224 NW_003726214.1 111759 111087 0.9939870614447158 1.010043026120346 NW_003726215.1 108801 113816 1.0460933263481034 1.0381526106828685 NW_003726216.1 112014 116142 1.0368525362901067 1.0968715742551371 NW_003726217.1 106428 108596 1.0203705791708948 1.0342272442084657 NW_003726218.1 104912 103079 0.9825282141223121 1.0497057193133859 NW_003726219.1 104646 108071 1.0327293924278043 1.0171109436967845 NW_003726220.1 103248 100714 0.9754571517123818 1.0013833352221135 NW_003726221.1 129482 124143 0.95876646947066 1.0889250171654197 NW_003726222.1 118473 118263 0.9982274442277987 1.121278960794238 NW_003726223.1 99993 102261 1.0226815877111397 1.0002677334957828 NW_003726224.1 109585 107150 0.9777798056303326 1.0433642184048586 NW_003726225.1 124049 122146 0.9846592878620545 1.1091798053050927 NW_003726226.1 99658 97532 0.9786670412811816 1.0432309523088394 NW_003726227.1 101741 101492 0.9975526090759871 1.0942992252488477 NW_003726228.1 97365 99313 1.0200071894417913 1.0716562227779751 NW_003726229.1 94395 96237 1.0195137454314318 1.0248104759417311 NW_003726230.1 102992 98593 0.9572879446947336 1.0269523405553584 NW_003726231.1 95509 90261 0.9450522987362447 0.9966525390166884 NW_003726232.1 92047 92240 1.0020967549186828 0.9827839694145327 NW_003726233.1 87753 87731 0.9997492963203537 0.9782191134945282 NW_003726234.1 96536 91991 0.9529191182564017 1.0840812045947332 NW_003726235.1 86544 86657 1.001305694213348 1.0353459349517489 NW_003726236.1 85476 85064 0.9951799335485985 1.0796470891209833 NW_003726237.1 110512 104483 0.9454448385695671 1.1724039597678018 NW_003726238.1 83291 82192 0.9868052970909222 0.9671576145021199 NW_003726239.1 82459 85758 1.0400077614329546 0.994479330361873 NW_003726240.1 81605 84731 1.038306476318853 1.025018226971141 NW_003726241.1 82380 87605 1.0634255887351298 1.0703001227025768 NW_003726242.1 102198 99085 0.9695395213213566 1.155991835141478 NW_003726243.1 82108 83052 1.0114970526623472 1.0118186796117123 NW_003726244.1 87041 82595 0.9489206236141589 1.040325715426741 NW_003726245.1 79722 74975 0.9404555831514513 1.011497051316224 NW_003726246.1 230124 225600 0.9803410335297492 1.7316990407334119 NW_003726247.1 78357 77778 0.9926107431371798 0.9577534868228733 NW_003726248.1 256406 251600 0.981256288854395 1.8021970297986456 NW_003726249.1 78050 77114 0.9880076873798846 1.0277992789151658 NW_003726250.1 81930 82969 1.012681557427072 1.1161138489960296 NW_003726251.1 77100 78408 1.0169649805447472 0.9709468489905753 NW_003726252.1 77130 74879 0.9708155062880851 1.015357425465946 NW_003726253.1 79078 80898 1.0230152507650674 1.1345533986456071 NW_003726254.1 90550 91335 1.0086692435118718 1.1523769806817306 NW_003726255.1 82767 81120 0.9801007647975643 1.1049461074508353 NW_003726256.1 89070 74242 0.8335241944538003 1.0248559033145774 NW_003726257.1 97802 97824 1.0002249442751683 1.1284364991294915 NW_003726258.1 79712 79413 0.9962489963869932 1.0538327402230137 NW_003726259.1 79581 82408 1.035523554617308 1.0816852339452885 NW_003726260.1 73720 72797 0.9874796527400976 1.0275814418739246 NW_003726261.1 97799 95136 0.9727706827268172 1.1873419006270742 NW_003726262.1 73171 74723 1.0212105888945073 1.0609338247190274 NW_003726263.1 104732 102859 0.982116258641103 1.2534198358558686 NW_003726264.1 78935 73064 0.9256223475011085 1.0585576976451188 NW_003726265.1 72992 74922 1.0264412538360368 1.036467692570689 NW_003726266.1 68721 70757 1.0296270426798213 1.0137509012379562 NW_003726267.1 73611 73625 1.000190188966323 1.103192297604271 NW_003726268.1 68272 67534 0.9891902976329974 0.9931916897311757 NW_003726269.1 79297 74840 0.9437935861381893 1.143284391971988 NW_003726270.1 84443 83579 0.9897682460357875 1.116736980774266 NW_003726271.1 80679 79073 0.9800939525774984 1.0750231595588204 NW_003726272.1 68834 69778 1.0137141528895603 1.0532555527347687 NW_003726273.1 67496 66522 0.9855695152305322 0.9757532152983746 NW_003726274.1 66523 68164 1.0246681598845513 1.0008391346281245 NW_003726275.1 67057 67958 1.0134363302861744 0.9848167932350866 NW_003726276.1 66195 66582 1.005846363018355 1.0412638943767856 NW_003726277.1 87584 79443 0.9070492327365729 1.0935362474511658 NW_003726278.1 84679 76079 0.8984399910249294 1.1064285782160737 NW_003726279.1 65840 65986 1.002217496962333 1.0417682831772939 NW_003726280.1 65696 65052 0.9901972722844617 1.064484181669703 NW_003726281.1 66021 66615 1.0089971372745035 1.0549192228129698 NW_003726282.1 67300 66312 0.9853194650817236 1.0271327720393282 NW_003726283.1 88153 76747 0.8706113234943791 1.1192048252549318 NW_003726284.1 92437 81362 0.8801886690394539 1.1850874903282183 NW_003726285.1 70351 69628 0.9897229605833606 1.0339835604287633 NW_003726286.1 64646 59552 0.9212016211366519 0.9835332884894155 NW_003726287.1 69126 66787 0.966163238144837 1.0649331337587262 NW_003726288.1 227674 200861 0.8822307334170788 1.7518782188015214 NW_003726289.1 64123 62037 0.9674687709558193 1.0389437227916594 NW_003726290.1 61944 61837 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