BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_haploid_no_error_hi_variance/alignment/5X_haploid_no_error_hi_variance.sorted.bam outfile = results/5X_haploid_no_error_hi_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 = 80,365,077 (100%) number of supplementary alignments = 2,423 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,182,535 number of mapped paired reads (second in pair) = 40,182,542 number of mapped paired reads (both in pair) = 80,364,932 number of mapped paired reads (singletons) = 145 number of mapped bases = 11,991,190,460 bp number of sequenced bases = 11,933,579,422 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,934,339 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 558.8919 std insert size = 100,723.4489 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.2406 >>>>>>> ACTG content number of A's = 3,472,481,627 bp (29.1%) number of C's = 2,494,112,726 bp (20.9%) number of T's = 3,472,734,057 bp (29.1%) number of G's = 2,494,231,806 bp (20.9%) number of N's = 19,206 bp (0%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.0511 number of mismatches = 556,496,079 number of insertions = 39,944,739 mapped reads with insertion percentage = 39.65% number of deletions = 39,984,285 mapped reads with deletion percentage = 39.55% homopolymer indels = 27.92% >>>>>>> Coverage mean coverageData = 4.9736X std coverageData = 2.3553X There is a 97.96% of reference with a coverageData >= 1X There is a 94.34% of reference with a coverageData >= 2X There is a 85.86% of reference with a coverageData >= 3X There is a 72.09% of reference with a coverageData >= 4X There is a 55.1% of reference with a coverageData >= 5X There is a 38.18% of reference with a coverageData >= 6X There is a 24.02% of reference with a coverageData >= 7X There is a 13.78% of reference with a coverageData >= 8X There is a 7.27% of reference with a coverageData >= 9X There is a 3.54% of reference with a coverageData >= 10X There is a 1.61% of reference with a coverageData >= 11X There is a 0.7% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 610482267 4.976266002308386 2.3288876260214586 NC_006584.3 85426708 426184856 4.988894761109137 2.3359311870305963 NC_006585.3 91889043 457390130 4.977635146336218 2.319434646719656 NC_006586.3 88276631 439348995 4.976956981967288 2.314182685655708 NC_006587.3 88915250 442286862 4.974252020885056 2.3215620867366535 NC_006588.3 77573801 385944797 4.975195130634375 2.3358100599228973 NC_006589.3 80974532 402940112 4.9761338787360945 2.3261678535273256 NC_006590.3 74330416 369910615 4.976571300233272 2.318062695024924 NC_006591.3 61074082 304390608 4.983957155508289 2.3415185771678138 NC_006592.3 69331447 344949052 4.975362074874912 2.329695070640012 NC_006593.3 74389097 370102894 4.975230362051579 2.318232307328645 NC_006594.3 72498081 360492042 4.972435642813773 2.3096484109904205 NC_006595.3 63241923 314713605 4.9763446472049875 2.3231890683822862 NC_006596.3 60966679 303325585 4.975268293685474 2.31853891410985 NC_006597.3 64190966 319244829 4.973360721818706 2.3246734822260713 NC_006598.3 59632846 297122928 4.982538113307555 2.3434105728581502 NC_006599.3 64289059 319885797 4.975742404317972 2.3139714887871268 NC_006600.3 55844845 277860534 4.975580718327716 2.3387988370220367 NC_006601.3 53741614 267369077 4.975084615061989 2.3139922186788078 NC_006602.3 58134056 289144130 4.973747746071597 2.3257370754372464 NC_006603.3 50858623 253022637 4.975019418044409 2.324820437482297 NC_006604.3 61439934 305544342 4.973057783558166 2.311370611460077 NC_006605.3 52294480 260088225 4.973531145161019 2.310343081690967 NC_006606.3 47698779 237293402 4.974831787622907 2.323617143571809 NC_006607.3 51628933 256842685 4.974781969637064 2.3321963617899373 NC_006608.3 38964690 194030568 4.979651268879593 2.330930734717113 NC_006609.3 45876710 228150923 4.973131748113586 2.320599112583447 NC_006610.3 41182112 204810990 4.973299815220744 2.3267309780143317 NC_006611.3 41845238 208118623 4.973531826966786 2.319408805732231 NC_006612.3 40214260 199993257 4.973192519270527 2.321609842076606 NC_006613.3 39895921 198417242 4.973371638669527 2.3119798477096065 NC_006614.3 38810281 192981040 4.972420581031093 2.3079432871082917 NC_006615.3 31377067 156081293 4.974374851543645 2.33063647349903 NC_006616.3 42124431 209459663 4.97240337798272 2.3312362779984843 NC_006617.3 26524999 131887171 4.9721838255300215 2.3151082330593535 NC_006618.3 30810995 153245672 4.973733305269758 2.320196048336423 NC_006619.3 30902991 153713147 4.974054032504491 2.325311152267825 NC_006620.3 23914537 118951244 4.974014090258155 2.333976003252837 NC_006621.3 123869142 616103152 4.973822713650507 2.342657675836956 NW_003726127.1 2660953 13272645 4.98792913666645 2.471866242470094 NW_003726128.1 1881673 9374904 4.982217420348807 2.8913945678927226 NW_003726129.1 1415205 7048691 4.9806854837285055 2.7537523393264456 NW_003726130.1 1067467 5334309 4.997165251946899 3.0823292557600923 NW_003726131.1 866315 4332479 5.001043500343409 2.382033365886366 NW_003726132.1 881102 4429541 5.027273800309159 2.728804655934167 NW_003726133.1 822601 4130947 5.021811303414413 2.599533170301085 NW_003726134.1 741967 3701818 4.989194937241144 2.328520267609828 NW_003726135.1 745551 3702296 4.965852101331767 3.303987901047611 NW_003726136.1 602611 3020230 5.011906520126582 2.404073296675367 NW_003726137.1 573630 2859209 4.98441329777034 2.5035514721773615 NW_003726138.1 666183 3294525 4.9453753698308125 3.226228287764954 NW_003726139.1 557017 2791939 5.012304830911804 2.6994556476380462 NW_003726140.1 510604 2567497 5.02835269602275 2.3258192475162605 NW_003726141.1 497093 2490374 5.009875415666686 2.415528092620051 NW_003726142.1 492630 2459147 4.991874226092605 2.5871660311385902 NW_003726143.1 577062 2854313 4.946284801286517 3.507075833604384 NW_003726144.1 561270 2770952 4.936932314215975 3.4121479114963487 NW_003726145.1 407330 2043704 5.017317653990622 2.3927895447048444 NW_003726146.1 405216 2032929 5.016902096659559 2.2680596223609495 NW_003726147.1 508668 2518180 4.950537482208435 3.491484589187726 NW_003726148.1 540093 2662138 4.929036295600943 4.048029051940805 NW_003726149.1 448434 2215519 4.940568734752494 3.2509058472231764 NW_003726150.1 377800 1893489 5.011881948120699 2.5079432736814873 NW_003726151.1 384880 1921965 4.993673352733319 2.7333523032256304 NW_003726152.1 367143 1833620 4.994293776539386 2.5463530392789644 NW_003726153.1 399987 2007420 5.018713108176016 3.1067678054906023 NW_003726154.1 376204 1899087 5.048024476082126 2.7493642547680697 NW_003726155.1 416178 2057092 4.942817736641533 3.285672506760882 NW_003726156.1 365470 1827324 4.999928858729855 2.9730066475149024 NW_003726157.1 322752 1634074 5.062939966289907 2.390406167302099 NW_003726158.1 320591 1612786 5.030665240134627 2.4977265446261296 NW_003726159.1 310270 1546645 4.984835788184484 2.396013491737149 NW_003726160.1 433650 2135757 4.92507090971982 4.066935354725819 NW_003726161.1 273228 1367278 5.0041650196905145 2.336067356598992 NW_003726162.1 281659 1406248 4.992732346560913 2.710346651631272 NW_003726163.1 320442 1590624 4.963843690901942 3.187461059976886 NW_003726164.1 265648 1334746 5.024491055833283 2.3360728576927405 NW_003726165.1 241365 1226458 5.081341536676817 2.366571808015568 NW_003726166.1 234529 1170348 4.990205902041965 2.3656877712225444 NW_003726167.1 252720 1287220 5.093463121240899 2.843441774563985 NW_003726168.1 254975 1272914 4.992309049906853 3.0094233576525884 NW_003726169.1 226053 1126926 4.985229127682446 2.429031251483161 NW_003726170.1 223744 1144121 5.113527066647597 2.446782728588672 NW_003726171.1 227140 1131276 4.980523025446861 2.569961623745492 NW_003726172.1 219672 1106716 5.038038530172257 2.476830672202322 NW_003726173.1 214597 1090571 5.081948955484 2.3044718984795827 NW_003726174.1 386314 1918853 4.967081182664879 5.174145940182105 NW_003726175.1 204342 1025018 5.016188546652181 2.349461749103644 NW_003726176.1 201724 1020073 5.056775594376475 2.3337830653652514 NW_003726177.1 216332 1076607 4.9766423830039015 2.6442861055506066 NW_003726178.1 200877 1003469 4.9954399956192095 2.3421247911757654 NW_003726179.1 310654 1483713 4.776094948077282 4.320937736464827 NW_003726180.1 200932 996832 4.961041546393805 2.6082881891411676 NW_003726181.1 201410 995097 4.940653393575294 2.4868914961383557 NW_003726182.1 292533 1408641 4.815323399411349 4.16960870292439 NW_003726183.1 192561 959027 4.980380243143731 2.2875364096330446 NW_003726184.1 210134 1048030 4.9874365880818905 2.894725886828268 NW_003726185.1 197844 987117 4.989370413052709 2.8036755906093136 NW_003726186.1 196813 1029775 5.232250918384456 2.9575666046174303 NW_003726187.1 180359 894754 4.9609611940629526 2.280419392048354 NW_003726188.1 210247 1007733 4.793090983462308 3.2826735497250925 NW_003726189.1 177735 910034 5.120173291698315 2.4357790712417864 NW_003726190.1 172100 871495 5.0638872748402095 2.3405590254533717 NW_003726191.1 166866 872078 5.226217443937052 2.4991861513742797 NW_003726192.1 164926 822789 4.988837417993524 2.3642996530901854 NW_003726193.1 157598 793027 5.031961065495755 2.7242248456566385 NW_003726194.1 143980 717342 4.982233643561606 2.4025407636327496 NW_003726195.1 141074 696969 4.940449693068886 2.409307242619601 NW_003726196.1 139526 692737 4.964931267290684 2.3477004763080473 NW_003726197.1 142260 730054 5.131829045409813 2.5614638984307905 NW_003726198.1 138160 676737 4.898212217718587 2.3120000952503323 NW_003726199.1 142296 715092 5.025383707201889 2.5744915442059604 NW_003726200.1 133119 663683 4.9856369113349706 2.3124214309323237 NW_003726201.1 129748 647453 4.990080771957949 2.2792410828276997 NW_003726202.1 125962 665104 5.28019561455042 2.4219728076436864 NW_003726203.1 127429 633514 4.971505701214009 2.376585117862913 NW_003726204.1 128261 635533 4.9549980118664285 2.548047967268308 NW_003726205.1 131872 657807 4.988223428779422 2.759355801440791 NW_003726206.1 133432 695420 5.211793272977996 2.8857707736735034 NW_003726207.1 119670 595025 4.972215258627894 2.3193023185129835 NW_003726208.1 144750 699113 4.829796200345423 3.406390768797208 NW_003726209.1 120779 606871 5.024640045040942 2.5529169680966834 NW_003726210.1 115952 578198 4.9865289085138675 2.3367055768254916 NW_003726211.1 118237 563533 4.766130737417221 2.454269750360283 NW_003726212.1 111908 557149 4.978634235264682 2.3032670175719154 NW_003726213.1 117332 610247 5.201027852589234 2.7556920941582823 NW_003726214.1 111759 556542 4.979840549754382 2.300232054266926 NW_003726215.1 108801 557304 5.122232332423415 2.3755746964965287 NW_003726216.1 112014 556532 4.968414662452908 2.6431987405015 NW_003726217.1 106428 541651 5.089365580486338 2.3505728131879047 NW_003726218.1 104912 533881 5.088845889888669 2.372468352416796 NW_003726219.1 104646 524068 5.008007950614452 2.311622433201055 NW_003726220.1 103248 525644 5.0910816674415 2.5152748024030886 NW_003726221.1 129482 624932 4.826400580775706 3.5955348710698694 NW_003726222.1 118473 593587 5.0103145864458565 3.205969884638319 NW_003726223.1 99993 514332 5.1436800576040325 2.3648745172003527 NW_003726224.1 109585 537725 4.90692156773281 2.7436042028497973 NW_003726225.1 124049 585481 4.719755902909334 3.334686627432119 NW_003726226.1 99658 490753 4.924371350017059 2.4484039194325695 NW_003726227.1 101741 504409 4.957775134901367 2.71962577228812 NW_003726228.1 97365 493838 5.072027936116674 2.315349561780654 NW_003726229.1 94395 460667 4.8802055193601355 2.325493238741424 NW_003726230.1 102992 496491 4.820675392263476 2.883543371570932 NW_003726231.1 95509 462533 4.842821095394151 2.593742582285402 NW_003726232.1 92047 461678 5.01567677382207 2.513641831398329 NW_003726233.1 87753 444443 5.064704340592344 2.348051526835725 NW_003726234.1 96536 464607 4.812784867821331 3.064080304311883 NW_003726235.1 86544 441510 5.101566833056018 2.4833940420275686 NW_003726236.1 85476 421167 4.927312929945248 2.342275402821834 NW_003726237.1 110512 554699 5.019355364123353 3.8261931066969534 NW_003726238.1 83291 412574 4.953404329399335 2.423199702184746 NW_003726239.1 82459 419605 5.088650117027856 2.2852750259319756 NW_003726240.1 81605 418454 5.12779854175602 2.426178533669896 NW_003726241.1 82380 427506 5.189439184268026 2.498159393176474 NW_003726242.1 102198 479548 4.6923423158965925 3.5784347103350034 NW_003726243.1 82108 411448 5.011058605738783 2.4624215986446645 NW_003726244.1 87041 431017 4.951884743971232 2.72928280253225 NW_003726245.1 79722 402628 5.050400140488197 2.3248623317370454 NW_003726246.1 230124 1120576 4.869444299595001 7.234714570725613 NW_003726247.1 78357 393107 5.016871498398356 2.2664496474182823 NW_003726248.1 256406 1247128 4.863879940407011 7.847520542463366 NW_003726249.1 78050 400016 5.125124919923127 2.4491255848329376 NW_003726250.1 81930 403467 4.924533138044672 2.7033185904809556 NW_003726251.1 77100 383969 4.980142671854734 2.3789842041738383 NW_003726252.1 77130 380837 4.937598859069104 2.443524932580771 NW_003726253.1 79078 403240 5.099269076102076 2.550547288437007 NW_003726254.1 90550 438414 4.841678630590834 3.425337631358714 NW_003726255.1 82767 408916 4.940568100813126 2.901541880099376 NW_003726256.1 89070 402298 4.516649825979567 3.1876499772589026 NW_003726257.1 97802 482633 4.934796834420564 3.680537270003412 NW_003726258.1 79712 396426 4.973228623042955 2.7546899176948543 NW_003726259.1 79581 396744 4.9854110905869495 2.8406660139032285 NW_003726260.1 73720 369906 5.017715680954964 2.331894820445072 NW_003726261.1 97799 471345 4.819527807032792 3.850546203287774 NW_003726262.1 73171 363369 4.9660247912424325 2.307573382942425 NW_003726263.1 104732 503548 4.807967001489516 3.8899461943011415 NW_003726264.1 78935 386722 4.899246215240388 2.844049202791607 NW_003726265.1 72992 381322 5.224161551950899 2.4768648579870978 NW_003726266.1 68721 346391 5.040540737183685 2.346221352746444 NW_003726267.1 73611 363765 4.941720666748176 2.897456021219255 NW_003726268.1 68272 339409 4.97142313100539 2.298763220402317 NW_003726269.1 79297 397192 5.008915848014427 3.199444772554808 NW_003726270.1 84443 411642 4.874791279324515 3.506112203227625 NW_003726271.1 80679 377003 4.672876461036949 3.2004230157008142 NW_003726272.1 68834 342272 4.972426417177558 2.4672426057542878 NW_003726273.1 67496 335871 4.976161550314092 2.3589153734657584 NW_003726274.1 66523 335636 5.045412864723479 2.2848789098071287 NW_003726275.1 67057 334985 4.995526194133349 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