BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_hi_error_no_variance/alignment/5X_hi_error_no_variance.sorted.bam outfile = results/5X_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 = 80,365,282 number of mapped reads = 80,365,080 (100%) number of supplementary alignments = 1,558 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,182,541 number of mapped paired reads (second in pair) = 40,182,539 number of mapped paired reads (both in pair) = 80,364,944 number of mapped paired reads (singletons) = 136 number of mapped bases = 12,017,114,915 bp number of sequenced bases = 12,017,006,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,345,477 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 508.5398 std insert size = 86,427.1646 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 30.5429 >>>>>>> ACTG content number of A's = 3,527,279,634 bp (29.35%) number of C's = 2,532,972,604 bp (21.08%) number of T's = 3,475,764,448 bp (28.92%) number of G's = 2,480,969,950 bp (20.65%) number of N's = 19,549 bp (0%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.049 number of mismatches = 588,430,397 number of insertions = 70,079 mapped reads with insertion percentage = 0.09% number of deletions = 55,150 mapped reads with deletion percentage = 0.07% homopolymer indels = 25.61% >>>>>>> Coverage mean coverageData = 4.9843X std coverageData = 2.341X There is a 98.42% of reference with a coverageData >= 1X There is a 94.88% of reference with a coverageData >= 2X There is a 86.43% of reference with a coverageData >= 3X There is a 72.63% of reference with a coverageData >= 4X There is a 55.55% of reference with a coverageData >= 5X There is a 38.51% of reference with a coverageData >= 6X There is a 24.22% of reference with a coverageData >= 7X There is a 13.9% of reference with a coverageData >= 8X There is a 7.32% of reference with a coverageData >= 9X There is a 3.57% of reference with a coverageData >= 10X There is a 1.63% of reference with a coverageData >= 11X There is a 0.71% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 611859637 4.987493452922606 2.315548668069526 NC_006584.3 85426708 427016821 4.998633694277438 2.3219593560148684 NC_006585.3 91889043 458407855 4.988710732355761 2.3073834165715885 NC_006586.3 88276631 440316197 4.987913471686522 2.3016665500403066 NC_006587.3 88915250 443275786 4.985374117488282 2.3018016167581012 NC_006588.3 77573801 386806407 4.986302102174934 2.3180765817341795 NC_006589.3 80974532 403830944 4.987135263714769 2.3094998397999293 NC_006590.3 74330416 370750232 4.987867039517174 2.3084298019541514 NC_006591.3 61074082 305066327 4.9950210794818 2.3257273914625602 NC_006592.3 69331447 345650747 4.985482951192408 2.318338210557978 NC_006593.3 74389097 371007300 4.987388138345059 2.3044191857238845 NC_006594.3 72498081 361333678 4.984044722507896 2.295863047193272 NC_006595.3 63241923 315293064 4.985507224377096 2.3041867890909393 NC_006596.3 60966679 303985318 4.986089499806935 2.3004621937292398 NC_006597.3 64190966 319874925 4.9831766825257 2.310344250408225 NC_006598.3 59632846 297773941 4.993455133769735 2.320393508751164 NC_006599.3 64289059 320555263 4.986155778077262 2.300459440633803 NC_006600.3 55844845 278495687 4.986954247970426 2.3240751817905143 NC_006601.3 53741614 267890490 4.98478683576567 2.296869482292936 NC_006602.3 58134056 289742068 4.984033248944474 2.309203979239732 NC_006603.3 50858623 253536328 4.985119789814207 2.311901166959212 NC_006604.3 61439934 306129511 4.98258202881533 2.293619071957813 NC_006605.3 52294480 260571487 4.982772311723914 2.2937079477804736 NC_006606.3 47698779 237791605 4.98527656232039 2.3045759700086665 NC_006607.3 51628933 257264636 4.982954731991072 2.3118486616267058 NC_006608.3 38964690 194414373 4.989501340829351 2.3192644221142875 NC_006609.3 45876710 228661493 4.984260924551913 2.2999890232331697 NC_006610.3 41182112 205279149 4.984667833451573 2.3066492935920153 NC_006611.3 41845238 208471005 4.9819529046530935 2.304391499855906 NC_006612.3 40214260 200409868 4.983552302093835 2.2982205944140017 NC_006613.3 39895921 198813900 4.983313958336743 2.290409048829664 NC_006614.3 38810281 193381817 4.982747148880473 2.287577606450447 NC_006615.3 31377067 156406708 4.984745961118673 2.2978757270440355 NC_006616.3 42124431 209884120 4.9824796446508675 2.3046275332645427 NC_006617.3 26524999 132172933 4.98295713413599 2.2941429976156904 NC_006618.3 30810995 153575877 4.98445042102665 2.302312022850163 NC_006619.3 30902991 153970676 4.982387497702083 2.316999205440339 NC_006620.3 23914537 119228346 4.985601268383327 2.3162340398504058 NC_006621.3 123869142 617505004 4.985139914830443 2.3379013678167877 NW_003726127.1 2660953 13337763 5.012400820307612 2.517905084351029 NW_003726128.1 1881673 9403322 4.997319938161413 2.8624431887378257 NW_003726129.1 1415205 7066677 4.993394596542551 2.7706224145563416 NW_003726130.1 1067467 5336382 4.999107232354723 3.075020477952452 NW_003726131.1 866315 4333315 5.002008507298154 2.3088956922516948 NW_003726132.1 881102 4424394 5.021432251884572 2.6724937284775154 NW_003726133.1 822601 4136455 5.028507137725337 2.6074655003246594 NW_003726134.1 741967 3709714 4.999836919970834 2.254134461379274 NW_003726135.1 745551 3714599 4.982353990538542 3.2696204083989215 NW_003726136.1 602611 3023777 5.017792572654664 2.5037848222734618 NW_003726137.1 573630 2864085 4.992913550546519 2.4541034791884524 NW_003726138.1 666183 3316697 4.978657516027878 3.2128903874070605 NW_003726139.1 557017 2807538 5.0403093621918185 2.642957581299533 NW_003726140.1 510604 2589400 5.071248952221291 2.3589672791171674 NW_003726141.1 497093 2513209 5.055812493839181 2.4581740761267645 NW_003726142.1 492630 2464994 5.003743174390516 2.5420249757327764 NW_003726143.1 577062 2859067 4.954523084174664 3.5080946671711257 NW_003726144.1 561270 2769534 4.934405900903308 3.37852838594587 NW_003726145.1 407330 2034500 4.994721724400363 2.251672783105606 NW_003726146.1 405216 2050462 5.060170378267393 2.2442391925279455 NW_003726147.1 508668 2513859 4.942042746939064 3.4411658722036664 NW_003726148.1 540093 2682071 4.965942902426064 4.013272064153547 NW_003726149.1 448434 2234064 4.981923761356186 3.3381053083080827 NW_003726150.1 377800 1895529 5.017281630492324 2.4816247892103958 NW_003726151.1 384880 1916741 4.9801002909997925 2.721904089628836 NW_003726152.1 367143 1831854 4.989483661679509 2.4788688692517553 NW_003726153.1 399987 2011681 5.029365954393517 3.0136154564830906 NW_003726154.1 376204 1879009 4.994654495964955 2.6922941684579667 NW_003726155.1 416178 2071972 4.978571668853231 3.2800021479182164 NW_003726156.1 365470 1832770 5.0148302186225955 2.9611442979342506 NW_003726157.1 322752 1623631 5.0305838538568315 2.4503426284806067 NW_003726158.1 320591 1629960 5.084235053385778 2.4039021008269126 NW_003726159.1 310270 1546260 4.9835949334450635 2.4358768693756767 NW_003726160.1 433650 2138492 4.931377839271302 4.064829212433721 NW_003726161.1 273228 1370483 5.01589514983823 2.2663440137083604 NW_003726162.1 281659 1406448 4.99344242506009 2.6237417743513727 NW_003726163.1 320442 1614570 5.0385717228078715 3.3470517057028903 NW_003726164.1 265648 1332955 5.017749051376257 2.3194978564678452 NW_003726165.1 241365 1219717 5.053412880906511 2.406779224065286 NW_003726166.1 234529 1174389 5.0074361806002665 2.370734953605679 NW_003726167.1 252720 1292826 5.115645773979107 2.949803662949796 NW_003726168.1 254975 1288876 5.054911265810373 2.9942805926020255 NW_003726169.1 226053 1138205 5.035124506199874 2.4113038404535327 NW_003726170.1 223744 1139873 5.094541082665904 2.5783442937267944 NW_003726171.1 227140 1138446 5.012089460244783 2.4534165234868834 NW_003726172.1 219672 1109263 5.049633089333188 2.4160493423794334 NW_003726173.1 214597 1082711 5.045322162005992 2.338328110582084 NW_003726174.1 386314 1915683 4.958875422583701 5.205431688822666 NW_003726175.1 204342 1035081 5.065434418768535 2.3558017811246024 NW_003726176.1 201724 1015706 5.03512720350578 2.38296359677015 NW_003726177.1 216332 1081741 5.000374424495683 2.7252126046468637 NW_003726178.1 200877 1003827 4.997222180737467 2.3050927396264056 NW_003726179.1 310654 1504619 4.843391683351896 4.3464777634673935 NW_003726180.1 200932 995035 4.952098222284156 2.4565979290131903 NW_003726181.1 201410 1013567 5.032356883968025 2.42998141042021 NW_003726182.1 292533 1418010 4.847350555321964 4.1243481483563755 NW_003726183.1 192561 961771 4.9946302730043985 2.3429746135751426 NW_003726184.1 210134 1071168 5.097547279355078 2.8735290658765584 NW_003726185.1 197844 1003000 5.069650836012212 2.716839648091797 NW_003726186.1 196813 1006714 5.115078780365118 2.795164617952718 NW_003726187.1 180359 898388 4.981109897482244 2.277088864078229 NW_003726188.1 210247 1003164 4.77135940108539 3.1502007848706266 NW_003726189.1 177735 922179 5.188505359102034 2.5194731479431285 NW_003726190.1 172100 887240 5.155374782103428 2.388911546370323 NW_003726191.1 166866 852389 5.108224563422147 2.50138450456292 NW_003726192.1 164926 838614 5.084789541976401 2.319488726536031 NW_003726193.1 157598 784859 4.980132996611633 2.799138814977028 NW_003726194.1 143980 718274 4.988706764828448 2.3785625439995894 NW_003726195.1 141074 708014 5.018741936855834 2.2520615213335837 NW_003726196.1 139526 693373 4.969489557501827 2.220058831607774 NW_003726197.1 142260 726523 5.1070082946717275 2.7080337660789446 NW_003726198.1 138160 697197 5.0463013896931095 2.2557578736301003 NW_003726199.1 142296 714016 5.017822004834992 2.5105181994698045 NW_003726200.1 133119 667728 5.016023257386248 2.351922319493622 NW_003726201.1 129748 648843 5.00079384653328 2.2729629151253437 NW_003726202.1 125962 666342 5.29002397548467 2.5115992080704026 NW_003726203.1 127429 635369 4.986062827142958 2.4412809270234423 NW_003726204.1 128261 644460 5.0245982800695455 2.472038821488249 NW_003726205.1 131872 658898 4.996496602766319 2.733084918610272 NW_003726206.1 133432 693545 5.197741171533066 2.8960964299938046 NW_003726207.1 119670 604653 5.052669842065681 2.2715281615478125 NW_003726208.1 144750 698055 4.822487046632125 3.3009804577736537 NW_003726209.1 120779 610779 5.056996663327234 2.572804121726334 NW_003726210.1 115952 583946 5.036101145301504 2.275008180751645 NW_003726211.1 118237 580513 4.909740605732554 2.51242953020907 NW_003726212.1 111908 555410 4.9630946849197555 2.2609763834166223 NW_003726213.1 117332 611184 5.209013738792486 2.7716379941337164 NW_003726214.1 111759 557394 4.9874640968512605 2.367841694199169 NW_003726215.1 108801 559719 5.144428819588056 2.308661944248694 NW_003726216.1 112014 569940 5.088113985751781 2.54071953793839 NW_003726217.1 106428 540367 5.077301086180328 2.2975401696342748 NW_003726218.1 104912 526688 5.020283666310813 2.23644911233285 NW_003726219.1 104646 525611 5.02275290025419 2.285858427925694 NW_003726220.1 103248 508179 4.9219258484425845 2.4766250551969358 NW_003726221.1 129482 624949 4.826531873156115 3.4878670486087344 NW_003726222.1 118473 583013 4.921062182944637 3.1973975010197235 NW_003726223.1 99993 503965 5.040002800196014 2.3647590435910337 NW_003726224.1 109585 550528 5.023753250901127 2.7497341085333336 NW_003726225.1 124049 593615 4.785326766036002 3.345719668123241 NW_003726226.1 99658 482287 4.83942081920167 2.374996881884157 NW_003726227.1 101741 506311 4.976469663164309 2.6010889365508882 NW_003726228.1 97365 493385 5.067375340214657 2.2273254598437426 NW_003726229.1 94395 470385 4.983155887494041 2.371461094442568 NW_003726230.1 102992 493546 4.792080938325307 2.9168914837075377 NW_003726231.1 95509 467960 4.899642965584396 2.6389010910802915 NW_003726232.1 92047 458359 4.979619107629798 2.389158762850866 NW_003726233.1 87753 431552 4.917803379941427 2.188208290805133 NW_003726234.1 96536 464285 4.809449324604293 3.02272303488079 NW_003726235.1 86544 436083 5.038858846367166 2.421446764163315 NW_003726236.1 85476 432417 5.058928822125509 2.236589888398478 NW_003726237.1 110512 530691 4.802111987838424 3.672335831280304 NW_003726238.1 83291 419745 5.039500066033545 2.313397500617396 NW_003726239.1 82459 426557 5.172958682496756 2.438115892993494 NW_003726240.1 81605 424540 5.202377305312175 2.482011164375048 NW_003726241.1 82380 433791 5.265731973780044 2.4450185594938136 NW_003726242.1 102198 483963 4.7355427699172195 3.613815362205393 NW_003726243.1 82108 405386 4.937229015443075 2.3341723170185187 NW_003726244.1 87041 428784 4.9262301673923785 3.0389152411806006 NW_003726245.1 79722 398516 4.998820902636663 2.304629644111245 NW_003726246.1 230124 1129388 4.907736698475604 7.330812902611999 NW_003726247.1 78357 395054 5.041719310336026 2.1792277852558413 NW_003726248.1 256406 1253534 4.888863755138336 7.9625834516403975 NW_003726249.1 78050 407474 5.220679051889814 2.3814555491954628 NW_003726250.1 81930 412768 5.038056877822531 2.5686319358280776 NW_003726251.1 77100 386511 5.013112840466926 2.314805506799737 NW_003726252.1 77130 386114 5.006015817451057 2.3652791877742487 NW_003726253.1 79078 388552 4.913528414982675 2.5359771056625577 NW_003726254.1 90550 444187 4.905433462175593 3.3123540488843823 NW_003726255.1 82767 415184 5.016298766416567 2.9772987670432807 NW_003726256.1 89070 418034 4.693319860783653 3.3067539020585173 NW_003726257.1 97802 483452 4.943170896300689 3.591537273793405 NW_003726258.1 79712 397170 4.982562224006423 2.833591245105287 NW_003726259.1 79581 408423 5.132167225845365 2.9286674875160448 NW_003726260.1 73720 368576 4.999674443841562 2.282928076266202 NW_003726261.1 97799 483599 4.944825611713822 3.8859473366669266 NW_003726262.1 73171 365061 4.989148706454743 2.294427561126982 NW_003726263.1 104732 505128 4.8230531260741705 3.9120922162067853 NW_003726264.1 78935 379174 4.803623234306708 2.81283602946808 NW_003726265.1 72992 379223 5.195404975887769 2.4566251429723533 NW_003726266.1 68721 344601 5.0144933863011305 2.326438025397262 NW_003726267.1 73611 364000 4.944913124397169 2.8835483915347075 NW_003726268.1 68272 340308 4.984591047574408 2.262622027307777 NW_003726269.1 79297 393231 4.9589643996620305 3.2736098043646953 NW_003726270.1 84443 412625 4.886432267920372 3.4371392755566763 NW_003726271.1 80679 384900 4.770758189863534 3.154810384870615 NW_003726272.1 68834 342796 4.98003893424761 2.462197601631234 NW_003726273.1 67496 336186 4.980828493540358 2.455787537421153 NW_003726274.1 66523 339317 5.100747110022097 2.373400322983566 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