BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_haploid_no_error_med_variance/alignment/5X_haploid_no_error_med_variance.sorted.bam outfile = results/5X_haploid_no_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 = 80,365,282 number of mapped reads = 80,365,282 (100%) number of supplementary alignments = 38 (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 = 12,052,319,756 bp number of sequenced bases = 12,040,242,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,368,660 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 357.9767 std insert size = 19,291.197 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 31.857 >>>>>>> ACTG content number of A's = 3,527,905,131 bp (29.3%) number of C's = 2,492,234,787 bp (20.7%) number of T's = 3,528,014,478 bp (29.3%) number of G's = 2,492,068,018 bp (20.7%) number of N's = 20,380 bp (0%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 114,432,619 number of insertions = 8,441,442 mapped reads with insertion percentage = 10% number of deletions = 8,491,214 mapped reads with deletion percentage = 10.05% homopolymer indels = 28.62% >>>>>>> Coverage mean coverageData = 4.9989X std coverageData = 2.3359X There is a 98.36% of reference with a coverageData >= 1X There is a 94.88% of reference with a coverageData >= 2X There is a 86.51% of reference with a coverageData >= 3X There is a 72.81% of reference with a coverageData >= 4X There is a 55.79% of reference with a coverageData >= 5X There is a 38.74% of reference with a coverageData >= 6X There is a 24.42% of reference with a coverageData >= 7X There is a 14.03% of reference with a coverageData >= 8X There is a 7.4% of reference with a coverageData >= 9X There is a 3.61% of reference with a coverageData >= 10X There is a 1.64% 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 0.11% 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 613844716 5.0036745636174995 2.312214416173329 NC_006584.3 85426708 428376133 5.014545720291598 2.315958914967697 NC_006585.3 91889043 459778061 5.003622259946705 2.3012738429670656 NC_006586.3 88276631 441805941 5.004789330938558 2.297705044447876 NC_006587.3 88915250 444712130 5.001528196794138 2.3066464818112165 NC_006588.3 77573801 388090694 5.002857781843125 2.324237795684702 NC_006589.3 80974532 404984785 5.001384694634605 2.304000946523863 NC_006590.3 74330416 371691286 5.00052745567844 2.3013929389646317 NC_006591.3 61074082 305804679 5.007110528488991 2.3249743009165673 NC_006592.3 69331447 346609742 4.999314986170705 2.313414351849574 NC_006593.3 74389097 371956969 5.000154377462063 2.3000662337286712 NC_006594.3 72498081 362362600 4.998237125752335 2.2949244070301926 NC_006595.3 63241923 316133490 4.998796288974325 2.303272011340848 NC_006596.3 60966679 304852192 5.000308315957311 2.3005570913137605 NC_006597.3 64190966 320842972 4.998257418341391 2.315453058560086 NC_006598.3 59632846 298600373 5.007313804878606 2.3265363666565513 NC_006599.3 64289059 321496056 5.000789574474873 2.295048663389277 NC_006600.3 55844845 279257117 5.000588989010534 2.3170703465755587 NC_006601.3 53741614 268651012 4.998938290167467 2.293528854803284 NC_006602.3 58134056 290581615 4.998474818271754 2.3093643346074213 NC_006603.3 50858623 254239788 4.998951465909724 2.306518340694333 NC_006604.3 61439934 307064776 4.997804457276923 2.2923665247542933 NC_006605.3 52294480 261334015 4.99735373599661 2.2912559433413366 NC_006606.3 47698779 238524879 5.000649576375949 2.3075236174541387 NC_006607.3 51628933 258039160 4.997956475296516 2.3085643230525785 NC_006608.3 38964690 194940287 5.002998535340587 2.3089702783363744 NC_006609.3 45876710 229240230 4.996875974759306 2.295784873714267 NC_006610.3 41182112 205836697 4.998206430015051 2.3177673003254835 NC_006611.3 41845238 209097884 4.996933796863576 2.2968120883069556 NC_006612.3 40214260 200999093 4.9982044429015975 2.300513705600752 NC_006613.3 39895921 199417558 4.998444778352153 2.2980901152011097 NC_006614.3 38810281 193974538 4.998019416556144 2.288228870779638 NC_006615.3 31377067 156903337 5.000573731126622 2.3084620514969387 NC_006616.3 42124431 210533120 4.997886380946012 2.305440364018931 NC_006617.3 26524999 132589686 4.99866884066612 2.3028971209060685 NC_006618.3 30810995 154005705 4.998400895524471 2.303107873245218 NC_006619.3 30902991 154460718 4.998244927165788 2.312652818826497 NC_006620.3 23914537 119559371 4.99944326749876 2.317739467741175 NC_006621.3 123869142 619033342 4.9974782419983175 2.3116877098799846 NW_003726127.1 2660953 13351601 5.0176012127985725 2.440265153455722 NW_003726128.1 1881673 9406700 4.999115149125273 2.8402527465548335 NW_003726129.1 1415205 7092983 5.01198271628492 2.7714265290950895 NW_003726130.1 1067467 5344743 5.006939792986575 3.049707357622533 NW_003726131.1 866315 4368526 5.042653076536825 2.310225829983622 NW_003726132.1 881102 4456428 5.05778899605267 2.7127090746729117 NW_003726133.1 822601 4118980 5.0072635457530446 2.589178987595109 NW_003726134.1 741967 3716576 5.009085309724018 2.27098866946224 NW_003726135.1 745551 3716515 4.98492390191952 3.2638398067516516 NW_003726136.1 602611 3009360 4.993868349565474 2.2664133168759166 NW_003726137.1 573630 2870865 5.004733016055646 2.4166000661934732 NW_003726138.1 666183 3323770 4.989274718808495 3.1760226602798856 NW_003726139.1 557017 2807129 5.039575093758359 2.6521303528557763 NW_003726140.1 510604 2574494 5.042056074766355 2.373622068052077 NW_003726141.1 497093 2516741 5.0629178041131135 2.4192889273667446 NW_003726142.1 492630 2446947 4.96710918945253 2.5651182230834135 NW_003726143.1 577062 2880705 4.992019921602878 3.5065678718438034 NW_003726144.1 561270 2785681 4.963174586206282 3.3857765837618476 NW_003726145.1 407330 2059511 5.056124027201532 2.336892596857446 NW_003726146.1 405216 2048549 5.05544943931138 2.3079681305420747 NW_003726147.1 508668 2542582 4.998509833525993 3.5180553655209934 NW_003726148.1 540093 2674292 4.951539827400096 4.015682044644616 NW_003726149.1 448434 2223945 4.9593585678159995 3.2287547342202934 NW_003726150.1 377800 1878826 4.973070407623081 2.4747292567495434 NW_003726151.1 384880 1924475 5.000194865932238 2.720760992071298 NW_003726152.1 367143 1843341 5.020771198143502 2.4394527108860666 NW_003726153.1 399987 2011532 5.0289934422868745 3.019677047138548 NW_003726154.1 376204 1887267 5.016605352415179 2.706284404138164 NW_003726155.1 416178 2077262 4.991282576205374 3.3355211730276317 NW_003726156.1 365470 1825917 4.996079021533915 2.9298826594291785 NW_003726157.1 322752 1632385 5.057706846123339 2.4116890518677723 NW_003726158.1 320591 1629091 5.081524434559922 2.4369959194680066 NW_003726159.1 310270 1552809 5.004702356012505 2.444328731230029 NW_003726160.1 433650 2169785 5.003539720973135 4.088945763161207 NW_003726161.1 273228 1366838 5.002554643008769 2.319702970294004 NW_003726162.1 281659 1415795 5.026627943719178 2.508975459549109 NW_003726163.1 320442 1610943 5.0272529818188625 3.1989095515893524 NW_003726164.1 265648 1333908 5.021336505450822 2.3315630129729192 NW_003726165.1 241365 1225503 5.077384873531788 2.400839492266754 NW_003726166.1 234529 1198172 5.108843682444388 2.4325915446760975 NW_003726167.1 252720 1286863 5.0920504906616015 2.9042850246022303 NW_003726168.1 254975 1283192 5.032618884204334 2.973838031448645 NW_003726169.1 226053 1123254 4.968985149500338 2.399198422437999 NW_003726170.1 223744 1135109 5.073248891590389 2.334608660979807 NW_003726171.1 227140 1137315 5.00711015232896 2.461869450314246 NW_003726172.1 219672 1094118 4.9806893914563535 2.3927072916852112 NW_003726173.1 214597 1088753 5.07347726203069 2.362186681048658 NW_003726174.1 386314 1925588 4.9845151871275695 5.2050298531912365 NW_003726175.1 204342 1026597 5.023915788237367 2.2742909469070227 NW_003726176.1 201724 1010869 5.011148896512066 2.365242447818623 NW_003726177.1 216332 1094418 5.0589741693323225 2.73329826807935 NW_003726178.1 200877 1011258 5.034214967368091 2.284789682568111 NW_003726179.1 310654 1504960 4.8444893675922405 4.327294482017741 NW_003726180.1 200932 994117 4.947529512471881 2.4436124573894826 NW_003726181.1 201410 1015753 5.043210366913262 2.3549226394165226 NW_003726182.1 292533 1423693 4.866777423401804 4.098722679296809 NW_003726183.1 192561 971285 5.044037993155416 2.3610130096858457 NW_003726184.1 210134 1067072 5.078054955409406 2.921568097085256 NW_003726185.1 197844 994908 5.028749924182689 2.6995597910729074 NW_003726186.1 196813 1030792 5.237418259972665 2.7402975806044627 NW_003726187.1 180359 911839 5.055688931519913 2.3084998352356783 NW_003726188.1 210247 1002282 4.767164335281835 3.1652136878176638 NW_003726189.1 177735 932754 5.248004050974766 2.4620935853379193 NW_003726190.1 172100 872366 5.068948285880302 2.3592027566368636 NW_003726191.1 166866 835570 5.0074311123895825 2.3077228640604295 NW_003726192.1 164926 840316 5.095109321756424 2.285117203749129 NW_003726193.1 157598 776296 4.925798550743029 2.6697200287520872 NW_003726194.1 143980 719803 4.999326295318794 2.413176436821296 NW_003726195.1 141074 701223 4.97060408012816 2.416771402028989 NW_003726196.1 139526 698202 5.00409959434084 2.2854818423338132 NW_003726197.1 142260 731432 5.141515534936032 2.494714868272949 NW_003726198.1 138160 699684 5.064302258251303 2.312624326920869 NW_003726199.1 142296 723192 5.082307303086524 2.572641314000715 NW_003726200.1 133119 663432 4.983751380343903 2.274048581275983 NW_003726201.1 129748 648630 4.999152202731449 2.309712432299828 NW_003726202.1 125962 644130 5.1136850796271895 2.3470792599954913 NW_003726203.1 127429 639417 5.017829536447747 2.3440803647404724 NW_003726204.1 128261 643685 5.018555913332969 2.5417694057223135 NW_003726205.1 131872 654985 4.966823889832565 2.7448169657710593 NW_003726206.1 133432 680104 5.097008213921698 2.922749952042992 NW_003726207.1 119670 609150 5.09024818250188 2.2558298882051946 NW_003726208.1 144750 713969 4.932428324697755 3.4076213768135557 NW_003726209.1 120779 611739 5.064945064953345 2.5751525383910354 NW_003726210.1 115952 583149 5.0292276114254175 2.203608300658323 NW_003726211.1 118237 567196 4.797110887454858 2.548759371690669 NW_003726212.1 111908 562462 5.026110733817064 2.3498878433915773 NW_003726213.1 117332 611415 5.210982511164899 2.662483109044812 NW_003726214.1 111759 558657 4.998765200118111 2.3271932479301745 NW_003726215.1 108801 553373 5.086102149796417 2.2740197824809774 NW_003726216.1 112014 568439 5.074713875051333 2.6041789695958726 NW_003726217.1 106428 547879 5.147884015484647 2.341003658242429 NW_003726218.1 104912 525210 5.006195668750953 2.445699755439346 NW_003726219.1 104646 523787 5.005322707031325 2.355805165640969 NW_003726220.1 103248 516414 5.001685262668526 2.3107936517319247 NW_003726221.1 129482 640858 4.949398371974483 3.644080738462902 NW_003726222.1 118473 587960 4.962818532492635 3.051760846024939 NW_003726223.1 99993 502086 5.021211484803937 2.2947471464896845 NW_003726224.1 109585 556100 5.074599625861204 2.7931872862856695 NW_003726225.1 124049 586256 4.726003434126837 3.2606168677802514 NW_003726226.1 99658 500486 5.022035360934396 2.48477737134776 NW_003726227.1 101741 508409 4.9970906517529805 2.665824973954427 NW_003726228.1 97365 485493 4.986319519334463 2.226110458289608 NW_003726229.1 94395 476445 5.04735420308279 2.348490168398628 NW_003726230.1 102992 497009 4.825704909119155 2.825333559847164 NW_003726231.1 95509 472740 4.949690605073868 2.560452466390567 NW_003726232.1 92047 459011 4.986702445489804 2.4002992445829783 NW_003726233.1 87753 434341 4.949585769147493 2.1977318225225657 NW_003726234.1 96536 477784 4.949283168973233 3.025403766798569 NW_003726235.1 86544 441816 5.105102606766501 2.475253886131103 NW_003726236.1 85476 423195 4.951038888108942 2.2507847370860725 NW_003726237.1 110512 535263 4.843483060663095 3.765559193504321 NW_003726238.1 83291 418208 5.021046691719394 2.333631301270425 NW_003726239.1 82459 426740 5.1751779672322 2.389705440122683 NW_003726240.1 81605 420816 5.1567428466392995 2.524615685845294 NW_003726241.1 82380 423215 5.137351298858946 2.6267177751245088 NW_003726242.1 102198 483353 4.7295739642654455 3.5413822045151973 NW_003726243.1 82108 410060 4.994154041019145 2.418377236760873 NW_003726244.1 87041 429804 4.937948782757551 2.7349749149494 NW_003726245.1 79722 397424 4.985123303479591 2.2591319901777696 NW_003726246.1 230124 1129013 4.906107142236359 7.307025008511945 NW_003726247.1 78357 392430 5.008231555572571 2.379826461145949 NW_003726248.1 256406 1264086 4.930017238286156 7.940795316335939 NW_003726249.1 78050 392451 5.028199871877002 2.3283885356698284 NW_003726250.1 81930 410436 5.0095935554741855 2.603323049809513 NW_003726251.1 77100 391279 5.074954604409857 2.450343970515495 NW_003726252.1 77130 383851 4.976675742253338 2.2623520765228395 NW_003726253.1 79078 399584 5.053036242697084 2.6069680857288375 NW_003726254.1 90550 456146 5.037504141358365 3.430479252038376 NW_003726255.1 82767 416884 5.0368383534500465 2.863806105323553 NW_003726256.1 89070 404011 4.535881890647805 3.1508119073248464 NW_003726257.1 97802 482613 4.934592339624957 3.669168221095021 NW_003726258.1 79712 398606 5.000577077478924 2.8666643064669026 NW_003726259.1 79581 410574 5.15919629057187 2.776672843302183 NW_003726260.1 73720 374236 5.076451437873033 2.393705107439448 NW_003726261.1 97799 477831 4.885847503553206 3.7938736719757826 NW_003726262.1 73171 368979 5.042694510120129 2.2832203916322187 NW_003726263.1 104732 515868 4.925600580529351 4.006084440239217 NW_003726264.1 78935 374879 4.749211376448977 2.7950704392711203 NW_003726265.1 72992 375528 5.1447829899167035 2.547671516329655 NW_003726266.1 68721 347575 5.057769822907117 2.1431305354142274 NW_003726267.1 73611 368585 5.007200010867941 2.7422887536594818 NW_003726268.1 68272 341971 5.0089494961331145 2.1861755490625083 NW_003726269.1 79297 406348 5.124380493587399 3.218933077577524 NW_003726270.1 84443 413715 4.899340383453928 3.4663411512741735 NW_003726271.1 80679 388638 4.817089949057375 3.374675392303204 NW_003726272.1 68834 343141 4.985050992242206 2.4467778263743343 NW_003726273.1 67496 337619 5.00205938129667 2.425462197396192 NW_003726274.1 66523 338625 5.090344692813012 2.4577382013713382 NW_003726275.1 67057 333968 4.980359992245403 2.317711498755512 NW_003726276.1 66195 334443 5.052390663947428 2.2920994020699257 NW_003726277.1 87584 435486 4.972209535988308 3.6999768551247003 NW_003726278.1 84679 390494 4.61146210985014 3.515090876811108 NW_003726279.1 65840 327957 4.981120899149453 2.2551171291660173 NW_003726280.1 65696 333230 5.072302727715538 2.2014390615232395 NW_003726281.1 66021 329863 4.996334499628906 2.4809253535966955 NW_003726282.1 67300 332773 4.944621099554235 2.617871474881072 NW_003726283.1 88153 415289 4.711002461629213 3.786483919444229 NW_003726284.1 92437 461506 4.9926544565487845 4.244607984291939 NW_003726285.1 70351 350536 4.9826725988258875 3.110365894828057 NW_003726286.1 64646 334984 5.181820994338397 2.528586192056442 NW_003726287.1 69126 345978 5.005034285218297 2.8767977480930926 NW_003726288.1 227674 1038583 4.56171104298251 7.9387306056103 NW_003726289.1 64123 319152 4.977184473589819 2.488923374177581 NW_003726290.1 61944 309224 4.991992767661113 2.3871353316505908 NW_003726291.1 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