BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_haploid_low_error_low_variance/alignment/5X_haploid_low_error_low_variance.sorted.bam outfile = results/5X_haploid_low_error_low_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 = 80,365,282 (100%) number of supplementary alignments = 8 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,182,641 number of mapped paired reads (second in pair) = 40,182,641 number of mapped paired reads (both in pair) = 80,365,282 number of mapped paired reads (singletons) = 0 number of mapped bases = 12,054,597,706 bp number of sequenced bases = 12,053,383,721 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,343,396 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 353.6105 std insert size = 10,398.4048 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 32.3133 >>>>>>> ACTG content number of A's = 3,537,219,511 bp (29.35%) number of C's = 2,490,389,762 bp (20.66%) number of T's = 3,536,533,540 bp (29.34%) number of G's = 2,489,219,673 bp (20.65%) number of N's = 21,235 bp (0%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0021 number of mismatches = 23,514,095 number of insertions = 851,632 mapped reads with insertion percentage = 1.05% number of deletions = 858,006 mapped reads with deletion percentage = 1.06% homopolymer indels = 28.68% >>>>>>> Coverage mean coverageData = 4.9999X std coverageData = 2.3303X There is a 98.45% of reference with a coverageData >= 1X There is a 94.98% of reference with a coverageData >= 2X There is a 86.63% of reference with a coverageData >= 3X There is a 72.92% of reference with a coverageData >= 4X There is a 55.87% of reference with a coverageData >= 5X There is a 38.8% of reference with a coverageData >= 6X There is a 24.44% of reference with a coverageData >= 7X There is a 14.04% of reference with a coverageData >= 8X There is a 7.39% of reference with a coverageData >= 9X There is a 3.6% of reference with a coverageData >= 10X There is a 1.63% of reference with a coverageData >= 11X There is a 0.7% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.11% 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% 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 613902174 5.0041429249564215 2.3068494901284975 NC_006584.3 85426708 428321295 5.013903789901397 2.3164707986517428 NC_006585.3 91889043 459797931 5.0038384990036295 2.2992801323404266 NC_006586.3 88276631 441761757 5.004288813423339 2.291108462098641 NC_006587.3 88915250 444720813 5.00162585158339 2.29974537369844 NC_006588.3 77573801 388059037 5.002449693034895 2.315999474011294 NC_006589.3 80974532 404963696 5.00112425472246 2.3000282325477377 NC_006590.3 74330416 371722585 5.000948534984656 2.2943634882082335 NC_006591.3 61074082 305881166 5.008362892789776 2.3186289825678648 NC_006592.3 69331447 346659531 5.000033116285601 2.3080056935693096 NC_006593.3 74389097 372047167 5.001366893860803 2.2927150618119567 NC_006594.3 72498081 362444192 4.999362562438032 2.2883778260260623 NC_006595.3 63241923 316227644 5.0002850798828495 2.2998844651486303 NC_006596.3 60966679 304888528 5.000904313649756 2.293430927423044 NC_006597.3 64190966 320913434 4.999355111745786 2.3028221589928304 NC_006598.3 59632846 298663328 5.008369515015265 2.31418130559608 NC_006599.3 64289059 321632281 5.002908519784058 2.2909594885429674 NC_006600.3 55844845 279356934 5.002376387650463 2.3086939270544184 NC_006601.3 53741614 268719090 5.000205055248248 2.2856486749600076 NC_006602.3 58134056 290639484 4.999470258878892 2.309678883342451 NC_006603.3 50858623 254320976 5.000547812708181 2.302016532115777 NC_006604.3 61439934 307194516 4.999916113191137 2.28923305422587 NC_006605.3 52294480 261381864 4.998268727406793 2.28379652521011 NC_006606.3 47698779 238544950 5.001070362828365 2.3062159621383653 NC_006607.3 51628933 258111409 4.999355865053419 2.306239977886859 NC_006608.3 38964690 195007814 5.00473156593829 2.3026980606419034 NC_006609.3 45876710 229351544 4.999302347531024 2.2888229158282565 NC_006610.3 41182112 205887026 4.999428538293519 2.3003538514278126 NC_006611.3 41845238 209171220 4.998686349925887 2.292892101752333 NC_006612.3 40214260 201045752 4.999364702968549 2.2954066454499102 NC_006613.3 39895921 199488173 5.0002147587970205 2.294843926697314 NC_006614.3 38810281 194004716 4.99879699402331 2.2865642132731705 NC_006615.3 31377067 156953389 5.002168908904073 2.2958840785879384 NC_006616.3 42124431 210596796 4.999397997803222 2.2943818559854154 NC_006617.3 26524999 132624650 4.9999869934019605 2.2989622699895027 NC_006618.3 30810995 154027852 4.9991196973677745 2.2951653917394124 NC_006619.3 30902991 154489517 4.999176843432404 2.308980603951031 NC_006620.3 23914537 119578434 5.000240397712906 2.317384995681012 NC_006621.3 123869142 619210434 4.998907912028647 2.308743880174042 NW_003726127.1 2660953 13337359 5.012248995002918 2.451858795856912 NW_003726128.1 1881673 9414459 5.003238607345697 2.8986264768245653 NW_003726129.1 1415205 7064765 4.9920435555272915 2.732509359566531 NW_003726130.1 1067467 5343271 5.00556082764151 3.0523919656163234 NW_003726131.1 866315 4354921 5.026948627231434 2.313755218708809 NW_003726132.1 881102 4478901 5.083294556135385 2.737675353340022 NW_003726133.1 822601 4154268 5.050161621490856 2.6288278161971372 NW_003726134.1 741967 3713358 5.0047481896095105 2.2742873338205074 NW_003726135.1 745551 3714215 4.981838935230454 3.272882582480578 NW_003726136.1 602611 3008011 4.991629757837146 2.3424839907782844 NW_003726137.1 573630 2875323 5.012504576120496 2.4293742093023063 NW_003726138.1 666183 3326678 4.993639885737102 3.1671060971500236 NW_003726139.1 557017 2808360 5.0417850801681094 2.6202469676711564 NW_003726140.1 510604 2570600 5.034429812535742 2.28598873793586 NW_003726141.1 497093 2510001 5.049358973069426 2.457797110265274 NW_003726142.1 492630 2458417 4.990392383736273 2.555411809737006 NW_003726143.1 577062 2879226 4.989456938769145 3.492991185805513 NW_003726144.1 561270 2784008 4.960193846099026 3.3823237159620847 NW_003726145.1 407330 2056831 5.049544595291287 2.308015957172971 NW_003726146.1 405216 2046705 5.050898779909974 2.2404153362981116 NW_003726147.1 508668 2548979 5.011085816288817 3.4963955853576003 NW_003726148.1 540093 2716789 5.0302244243121095 4.037389975945797 NW_003726149.1 448434 2231422 4.976032147428607 3.2666656470324216 NW_003726150.1 377800 1898647 5.025534674430916 2.4842903210285385 NW_003726151.1 384880 1926557 5.005604344211183 2.708620142403931 NW_003726152.1 367143 1838911 5.008705054978578 2.480663093699235 NW_003726153.1 399987 2020361 5.051066659666439 3.0028966241725152 NW_003726154.1 376204 1897486 5.043768806285951 2.7383676588144983 NW_003726155.1 416178 2084336 5.00828011091408 3.279840034430644 NW_003726156.1 365470 1828858 5.004126193668427 2.993043618572314 NW_003726157.1 322752 1618781 5.015556836208606 2.3543885222674032 NW_003726158.1 320591 1626549 5.073595328627441 2.43593691179603 NW_003726159.1 310270 1549181 4.993009314468044 2.3897673364601304 NW_003726160.1 433650 2125886 4.902308313155771 3.9991611331402397 NW_003726161.1 273228 1367313 5.004293117835654 2.332552349435885 NW_003726162.1 281659 1428498 5.071728579594474 2.500010994989611 NW_003726163.1 320442 1616400 5.044282584679911 3.242953963582911 NW_003726164.1 265648 1345187 5.0637949466963805 2.340855751409862 NW_003726165.1 241365 1223117 5.06749943032337 2.305675303219921 NW_003726166.1 234529 1190035 5.0741486127515145 2.299795455201771 NW_003726167.1 252720 1288743 5.099489553656221 2.8824680891766903 NW_003726168.1 254975 1270877 4.984320031375625 2.9733917653558986 NW_003726169.1 226053 1149599 5.085528614970825 2.379490156725996 NW_003726170.1 223744 1133731 5.06709006721968 2.408251252711697 NW_003726171.1 227140 1140905 5.022915382583428 2.4093407680790815 NW_003726172.1 219672 1096755 4.992693652354419 2.4013325012983793 NW_003726173.1 214597 1094372 5.0996612254598155 2.3441934390837065 NW_003726174.1 386314 1927756 4.990127202224097 5.201788712600156 NW_003726175.1 204342 1019699 4.9901586555872015 2.2756190010590895 NW_003726176.1 201724 1018791 5.050420376355813 2.270874757309669 NW_003726177.1 216332 1085086 5.015836769409981 2.7264187270675486 NW_003726178.1 200877 1010406 5.029973565913469 2.2619194353535432 NW_003726179.1 310654 1517136 4.883684098707887 4.324773336520024 NW_003726180.1 200932 1002542 4.989459120498477 2.329495441706579 NW_003726181.1 201410 1029515 5.111538652499876 2.4390657386040395 NW_003726182.1 292533 1449887 4.956319457975681 4.249464162042324 NW_003726183.1 192561 965115 5.011996198607195 2.300215544095444 NW_003726184.1 210134 1069183 5.088100926075742 2.762806545098723 NW_003726185.1 197844 989055 4.999166009583308 2.7097702133413266 NW_003726186.1 196813 1025742 5.211759385812929 2.8215755293891083 NW_003726187.1 180359 920688 5.104752188690334 2.2816956112623767 NW_003726188.1 210247 1006416 4.786826922619586 3.2465388350375126 NW_003726189.1 177735 907129 5.103828733789068 2.483882546605375 NW_003726190.1 172100 876534 5.093166763509587 2.3719056400400724 NW_003726191.1 166866 850863 5.099079500916903 2.299327578326283 NW_003726192.1 164926 833012 5.050822793252731 2.3327069243510934 NW_003726193.1 157598 789870 5.011929085394485 2.715548189481747 NW_003726194.1 143980 719967 5.000465342408668 2.503652034584137 NW_003726195.1 141074 704119 4.991132313537576 2.4094673396479247 NW_003726196.1 139526 696319 4.990603901781747 2.294633384708778 NW_003726197.1 142260 732910 5.151904962744271 2.506500178915057 NW_003726198.1 138160 705286 5.104849449913144 2.3688858005949687 NW_003726199.1 142296 714898 5.02402035194243 2.5923775498476136 NW_003726200.1 133119 669549 5.02970274716607 2.3255416134027342 NW_003726201.1 129748 650719 5.015252643586028 2.1353511402689263 NW_003726202.1 125962 657258 5.217906987821724 2.4009560744539478 NW_003726203.1 127429 636019 4.9911637068485195 2.3743107531792513 NW_003726204.1 128261 644661 5.026165397119935 2.473108220829425 NW_003726205.1 131872 652206 4.94575042465421 2.714168992068153 NW_003726206.1 133432 684849 5.1325693986450025 2.7915397163572258 NW_003726207.1 119670 597272 4.990991894376201 2.327954170655726 NW_003726208.1 144750 702285 4.851709844559585 3.3568144328706198 NW_003726209.1 120779 604796 5.0074599061095055 2.533562740863831 NW_003726210.1 115952 577832 4.9833724299710225 2.3312572763083264 NW_003726211.1 118237 587693 4.970466097752818 2.4443476528841193 NW_003726212.1 111908 565480 5.053079315151732 2.305178352926073 NW_003726213.1 117332 604026 5.148007363720042 2.7239391731567233 NW_003726214.1 111759 558880 5.000760565144642 2.474268398422258 NW_003726215.1 108801 562183 5.167075670260384 2.4181688940663295 NW_003726216.1 112014 575907 5.141384112700198 2.5854903665941196 NW_003726217.1 106428 539996 5.073815161423686 2.3250273430180033 NW_003726218.1 104912 537886 5.127020741192618 2.2948164055274907 NW_003726219.1 104646 523185 4.99956997878562 2.3380947080813215 NW_003726220.1 103248 513266 4.97119556795289 2.3269802284311583 NW_003726221.1 129482 649742 5.018010225359509 3.692670438522672 NW_003726222.1 118473 590706 4.98599680939961 3.2003036310555815 NW_003726223.1 99993 509427 5.094626623863671 2.2797752416091766 NW_003726224.1 109585 544795 4.971437696765069 2.804567744397426 NW_003726225.1 124049 597616 4.8175801497795225 3.3079131387643184 NW_003726226.1 99658 500683 5.024012121455377 2.384357711117522 NW_003726227.1 101741 508191 4.994947956084568 2.7114749593430396 NW_003726228.1 97365 484779 4.978986288707441 2.209959471906469 NW_003726229.1 94395 479053 5.074982785105143 2.428969796758971 NW_003726230.1 102992 504587 4.899283439490445 2.843932208543412 NW_003726231.1 95509 476709 4.991246898198075 2.561538122000743 NW_003726232.1 92047 458432 4.980412180733755 2.510205561143113 NW_003726233.1 87753 433535 4.940400897974998 2.3398204595406606 NW_003726234.1 96536 481472 4.9874865335211735 3.075761352314586 NW_003726235.1 86544 434103 5.015980310593456 2.3805050772558154 NW_003726236.1 85476 425708 4.980438953624409 2.149620285790712 NW_003726237.1 110512 545078 4.93229694512813 3.7727345644977706 NW_003726238.1 83291 414887 4.9811744366137995 2.287876362847239 NW_003726239.1 82459 421149 5.107374574030731 2.305179880609236 NW_003726240.1 81605 426876 5.231003002267018 2.650927597260266 NW_003726241.1 82380 426591 5.178332119446468 2.5296852671675287 NW_003726242.1 102198 489848 4.793127067065892 3.6277368992528207 NW_003726243.1 82108 413713 5.0386442246796905 2.4699162065696116 NW_003726244.1 87041 425967 4.8938661090750335 2.730547213488702 NW_003726245.1 79722 402605 5.050111637941848 2.1943013340285105 NW_003726246.1 230124 1127915 4.901335801567851 7.324042172896432 NW_003726247.1 78357 392724 5.011983613461465 2.1722103404387565 NW_003726248.1 256406 1264196 4.930446245407674 7.9546487532102255 NW_003726249.1 78050 396526 5.08040999359385 2.2892900007974326 NW_003726250.1 81930 411572 5.023459050408886 2.619008501881666 NW_003726251.1 77100 385147 4.995421530479896 2.3638438388649767 NW_003726252.1 77130 388814 5.0410216517567745 2.3719418474150933 NW_003726253.1 79078 401713 5.079959027795342 2.619319727421181 NW_003726254.1 90550 448148 4.949177250138045 3.4486368877078712 NW_003726255.1 82767 413957 5.001474017422403 3.0143654374774176 NW_003726256.1 89070 409496 4.597462669810262 3.1552137993443328 NW_003726257.1 97802 485862 4.967812519171387 3.682605730933506 NW_003726258.1 79712 398675 5.00144269369731 2.6380205506698116 NW_003726259.1 79581 407370 5.118935424284691 2.940595838840696 NW_003726260.1 73720 373106 5.061123168746609 2.3248211520488407 NW_003726261.1 97799 478147 4.889078620435792 3.83933547858086 NW_003726262.1 73171 368063 5.030175889355072 2.266357040116242 NW_003726263.1 104732 518333 4.949136844517435 3.9774205100152535 NW_003726264.1 78935 373558 4.732476087920441 2.61596778181974 NW_003726265.1 72992 385223 5.277605765015344 2.6637511331951407 NW_003726266.1 68721 349490 5.085636122873648 2.3523891146110705 NW_003726267.1 73611 363012 4.931491217345234 2.809113871834232 NW_003726268.1 68272 341626 5.003896179985938 2.265179948949961 NW_003726269.1 79297 392972 4.955698197914171 3.206565877955167 NW_003726270.1 84443 417569 4.9449806378267 3.5006531254922373 NW_003726271.1 80679 379764 4.707098501468784 3.1694720648164085 NW_003726272.1 68834 340200 4.9423250138013195 2.427908329531087 NW_003726273.1 67496 337423 4.999155505511438 2.4272237070962444 NW_003726274.1 66523 338432 5.087443440614524 2.2732951133436767 NW_003726275.1 67057 340176 5.07293794831263 2.3340505767702346 NW_003726276.1 66195 329135 4.972203338620742 2.311417574764354 NW_003726277.1 87584 424020 4.841295213737669 3.7071431646090818 NW_003726278.1 84679 380393 4.492176336517908 3.494374282085163 NW_003726279.1 65840 330877 5.025470838396112 2.2246520143533606 NW_003726280.1 65696 329718 5.018844374086703 2.2441722663971806 NW_003726281.1 66021 327904 4.966662122657942 2.335916220520959 NW_003726282.1 67300 340209 5.055111441307578 2.5732257357803094 NW_003726283.1 88153 407354 4.620988508615702 3.775537039134472 NW_003726284.1 92437 449092 4.858357584084295 4.045011196935343 NW_003726285.1 70351 348004 4.946681639209109 3.068281710514068 NW_003726286.1 64646 330561 5.113402221328466 2.5953042468181455 NW_003726287.1 69126 344968 4.990423285015768 2.938368379775296 NW_003726288.1 227674 1032722 4.535968094731941 7.880631841474044 NW_003726289.1 64123 324878 5.066481605664114 2.5388688968113358 NW_003726290.1 61944 309014 4.988602608807955 2.2144815546705874 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