BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_haploid_hi_error_med_variance/alignment/5X_haploid_hi_error_med_variance.sorted.bam outfile = results/5X_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 = 80,365,282 number of mapped reads = 80,363,805 (100%) number of supplementary alignments = 3,572 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,181,890 number of mapped paired reads (second in pair) = 40,181,915 number of mapped paired reads (both in pair) = 80,363,036 number of mapped paired reads (singletons) = 769 number of mapped bases = 11,984,329,051 bp number of sequenced bases = 11,972,525,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,396,090 duplication rate = 1.74% >>>>>>> Insert size mean insert size = 632.5255 std insert size = 109,128.9163 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.0286 >>>>>>> ACTG content number of A's = 3,508,172,055 bp (29.3%) number of C's = 2,528,851,505 bp (21.12%) number of T's = 3,457,543,320 bp (28.88%) number of G's = 2,477,940,138 bp (20.7%) number of N's = 18,720 bp (0%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0582 number of mismatches = 685,700,747 number of insertions = 8,208,927 mapped reads with insertion percentage = 9.74% number of deletions = 8,243,501 mapped reads with deletion percentage = 9.77% homopolymer indels = 27.54% >>>>>>> Coverage mean coverageData = 4.9707X std coverageData = 2.3413X There is a 98.34% of reference with a coverageData >= 1X There is a 94.74% of reference with a coverageData >= 2X There is a 86.21% of reference with a coverageData >= 3X There is a 72.35% of reference with a coverageData >= 4X There is a 55.26% of reference with a coverageData >= 5X There is a 38.23% of reference with a coverageData >= 6X There is a 24% of reference with a coverageData >= 7X There is a 13.75% of reference with a coverageData >= 8X There is a 7.24% of reference with a coverageData >= 9X There is a 3.53% 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 0.3% 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 0.03% 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% 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 610130047 4.973394927248424 2.31325490015273 NC_006584.3 85426708 425846601 4.984935168050723 2.3152633945812107 NC_006585.3 91889043 457175867 4.9753033884573155 2.305405912699091 NC_006586.3 88276631 439119633 4.974358763192945 2.3027087371965425 NC_006587.3 88915250 442051041 4.971599821178032 2.3036345914570124 NC_006588.3 77573801 385695695 4.9719839691753664 2.320753374097122 NC_006589.3 80974532 402720866 4.973426286674926 2.30744223704907 NC_006590.3 74330416 369682089 4.9734968387638245 2.310529800646563 NC_006591.3 61074082 304211350 4.981022064318544 2.327614121097457 NC_006592.3 69331447 344694048 4.971684032499711 2.3162153723632826 NC_006593.3 74389097 369957123 4.973270787249911 2.3062371207622814 NC_006594.3 72498081 360363221 4.970658754402065 2.2991264546783774 NC_006595.3 63241923 314410774 4.97155619382415 2.3046129970333644 NC_006596.3 60966679 303218542 4.973512531328794 2.3051056249496233 NC_006597.3 64190966 319054219 4.970391300856884 2.3155879722543724 NC_006598.3 59632846 296937612 4.979430497078741 2.326544306471474 NC_006599.3 64289059 319674999 4.972463494915986 2.294500719477323 NC_006600.3 55844845 277795110 4.974409186738722 2.324642696891183 NC_006601.3 53741614 267212444 4.972170058011283 2.2985912091996363 NC_006602.3 58134056 288934541 4.9701424755224375 2.3089502313177515 NC_006603.3 50858623 252845695 4.971540322670553 2.3108811894765786 NC_006604.3 61439934 305403313 4.9707623872122 2.2974160916389064 NC_006605.3 52294480 259877683 4.9695050605723585 2.2938080255685076 NC_006606.3 47698779 237153730 4.971903578496213 2.30611630005341 NC_006607.3 51628933 256602306 4.970126072526039 2.3118232258757865 NC_006608.3 38964690 193904163 4.9764071778833605 2.3159803335723304 NC_006609.3 45876710 228019779 4.970273129873524 2.302855914337714 NC_006610.3 41182112 204725131 4.971214953715827 2.318441182557763 NC_006611.3 41845238 207917738 4.9687311612375105 2.3031695906045355 NC_006612.3 40214260 199896376 4.970783398724731 2.298690650520029 NC_006613.3 39895921 198269676 4.969672864551742 2.2932616139096584 NC_006614.3 38810281 192886471 4.969983881332887 2.2878982186864385 NC_006615.3 31377067 156028630 4.972696460124842 2.3100315874101303 NC_006616.3 42124431 209341482 4.969597856407841 2.306991085989463 NC_006617.3 26524999 131850136 4.970787595505659 2.3004393747881666 NC_006618.3 30810995 153160627 4.970973089314382 2.3041250600913386 NC_006619.3 30902991 153613197 4.970819717741884 2.311397158094708 NC_006620.3 23914537 118929098 4.9730880426411765 2.3167138755539343 NC_006621.3 123869142 615797149 4.971352340520773 2.334233234134341 NW_003726127.1 2660953 13355293 5.018988685632554 2.508378842243949 NW_003726128.1 1881673 9392721 4.991686121871335 2.845514801632373 NW_003726129.1 1415205 7040758 4.975079935415717 2.7720442657774056 NW_003726130.1 1067467 5338610 5.001194416314509 3.0725323408103455 NW_003726131.1 866315 4351254 5.022715755816303 2.3106093508799237 NW_003726132.1 881102 4454788 5.055927690551151 2.7306140225298416 NW_003726133.1 822601 4092339 4.974877249115914 2.6068996123270187 NW_003726134.1 741967 3696901 4.982567957874137 2.269417054533068 NW_003726135.1 745551 3698215 4.960378297393471 3.264435233412206 NW_003726136.1 602611 3020530 5.012404353720726 2.4203769609389885 NW_003726137.1 573630 2850792 4.969740076355839 2.4181077808760367 NW_003726138.1 666183 3282301 4.927026057404647 3.149991880691779 NW_003726139.1 557017 2787924 5.00509679237797 2.6385892602128593 NW_003726140.1 510604 2556934 5.007665431528151 2.3827477986747976 NW_003726141.1 497093 2511334 5.052040563838155 2.433159512659137 NW_003726142.1 492630 2423697 4.919913525363864 2.547518427062784 NW_003726143.1 577062 2853295 4.944520692750519 3.481826282566862 NW_003726144.1 561270 2757519 4.9129990913464106 3.37771546956719 NW_003726145.1 407330 2051723 5.037004394471313 2.315015188076705 NW_003726146.1 405216 2043693 5.0434657071783935 2.316006455999744 NW_003726147.1 508668 2517407 4.949017826951961 3.4803586935048973 NW_003726148.1 540093 2660050 4.925170294745534 4.0114568599042615 NW_003726149.1 448434 2214225 4.937683137317866 3.27668872034457 NW_003726150.1 377800 1879800 4.97564849126522 2.4995175753264296 NW_003726151.1 384880 1913695 4.9721861359384745 2.7222013711420763 NW_003726152.1 367143 1820962 4.959816747153017 2.422498097683537 NW_003726153.1 399987 1995678 4.989357154107508 3.0196308063509374 NW_003726154.1 376204 1872216 4.976597803319476 2.6987158093742556 NW_003726155.1 416178 2054018 4.935431474032746 3.3010066740595154 NW_003726156.1 365470 1830323 5.008134730620845 2.9762475138089157 NW_003726157.1 322752 1627729 5.043280909181043 2.477139199748059 NW_003726158.1 320591 1619974 5.053086331182098 2.418349391660834 NW_003726159.1 310270 1537210 4.954426789570374 2.4395538348152757 NW_003726160.1 433650 2135321 4.924065490603021 4.045153643971333 NW_003726161.1 273228 1364733 4.994850454565418 2.2731180716055124 NW_003726162.1 281659 1413246 5.017577993247153 2.683843155999279 NW_003726163.1 320442 1601558 4.9979653104149895 3.2466033349551275 NW_003726164.1 265648 1327210 4.996122688670722 2.323273466010911 NW_003726165.1 241365 1220774 5.057792140534046 2.387304161930926 NW_003726166.1 234529 1188796 5.068865683987908 2.379388488725292 NW_003726167.1 252720 1291244 5.1093858816081035 2.911878752487157 NW_003726168.1 254975 1280858 5.0234650455927055 3.049459458303533 NW_003726169.1 226053 1119793 4.953674580739915 2.42588605770109 NW_003726170.1 223744 1143309 5.1098979190503435 2.4119615698998835 NW_003726171.1 227140 1132456 4.985718059346659 2.4530914009188853 NW_003726172.1 219672 1084251 4.935772424341746 2.3991510007424126 NW_003726173.1 214597 1083220 5.047694049777024 2.3456777724780933 NW_003726174.1 386314 1914780 4.956537945816097 5.1787841566231565 NW_003726175.1 204342 1026235 5.022144248367932 2.299682053944946 NW_003726176.1 201724 1005044 4.982272808391664 2.4141666273802245 NW_003726177.1 216332 1078493 4.985360464471276 2.676576927208893 NW_003726178.1 200877 1010143 5.028664307013745 2.2765115648811114 NW_003726179.1 310654 1472751 4.740808101617877 4.251790861429232 NW_003726180.1 200932 983730 4.895835407003364 2.540695717808037 NW_003726181.1 201410 1020045 5.064520133061913 2.3762450502517916 NW_003726182.1 292533 1418487 4.848981140589267 4.112451874465607 NW_003726183.1 192561 961992 4.9957779612694155 2.3754571564801825 NW_003726184.1 210134 1059286 5.041002407987285 2.898426715110831 NW_003726185.1 197844 981267 4.959801661915448 2.6604329531113993 NW_003726186.1 196813 1021350 5.189443786741729 2.746753452163283 NW_003726187.1 180359 913832 5.066739114765551 2.2839922392558094 NW_003726188.1 210247 996902 4.741575385142237 3.1250754401293475 NW_003726189.1 177735 934024 5.255149520353335 2.4474389140376913 NW_003726190.1 172100 878420 5.1041255084253345 2.3532279087681456 NW_003726191.1 166866 840069 5.034392866132106 2.313733435036079 NW_003726192.1 164926 836206 5.070189054485041 2.289257266870515 NW_003726193.1 157598 773673 4.909154938514448 2.683580230464955 NW_003726194.1 143980 715795 4.971489095707737 2.4022872300922002 NW_003726195.1 141074 698579 4.951862143272325 2.375617228190294 NW_003726196.1 139526 695351 4.983666126743403 2.281676222485829 NW_003726197.1 142260 732655 5.150112470125123 2.6379241927189203 NW_003726198.1 138160 687427 4.975586276780544 2.287860190291619 NW_003726199.1 142296 707813 4.97422977455445 2.5559564944033513 NW_003726200.1 133119 663700 4.985764616621219 2.2832381539127664 NW_003726201.1 129748 641915 4.947398033110337 2.285826933698475 NW_003726202.1 125962 647212 5.138152776234103 2.3047706763061275 NW_003726203.1 127429 635303 4.985544891665162 2.3473934649258257 NW_003726204.1 128261 630364 4.9146973748840255 2.4750915947736045 NW_003726205.1 131872 655298 4.96919740354283 2.7836608137425665 NW_003726206.1 133432 675494 5.062458780502428 2.889193227077103 NW_003726207.1 119670 599170 5.006852176819587 2.256187417184141 NW_003726208.1 144750 684982 4.732172711571676 3.3030137350219704 NW_003726209.1 120779 603916 5.000173871285571 2.5142984101438177 NW_003726210.1 115952 579949 5.001629984821306 2.214690092515148 NW_003726211.1 118237 562546 4.75778309666179 2.471485468802727 NW_003726212.1 111908 562651 5.027799621117347 2.3890015472311625 NW_003726213.1 117332 607214 5.175178127024171 2.788246360430114 NW_003726214.1 111759 555892 4.974024463354182 2.318179420635789 NW_003726215.1 108801 553427 5.086598468764074 2.3077172238713453 NW_003726216.1 112014 567327 5.064786544539076 2.632905246584972 NW_003726217.1 106428 537934 5.0544405607546885 2.3458450312260837 NW_003726218.1 104912 525856 5.012353210309593 2.4315295889105903 NW_003726219.1 104646 518885 4.958479062744873 2.3123421214060507 NW_003726220.1 103248 512619 4.96492910274291 2.3051129201295266 NW_003726221.1 129482 627512 4.846326130272934 3.611320599804975 NW_003726222.1 118473 588700 4.969064681404202 3.0928820123133627 NW_003726223.1 99993 498697 4.987319112337864 2.2224710431752164 NW_003726224.1 109585 554757 5.062344298946024 2.815701671276645 NW_003726225.1 124049 587341 4.734749977831341 3.2802327192234433 NW_003726226.1 99658 496127 4.978295771538662 2.5284692485551767 NW_003726227.1 101741 505219 4.965736527063819 2.6532066787429818 NW_003726228.1 97365 496736 5.101792225132234 2.306163933449696 NW_003726229.1 94395 471258 4.992404258700143 2.3267220614436797 NW_003726230.1 102992 492167 4.778691548858164 2.7892643524505436 NW_003726231.1 95509 464518 4.863604477064989 2.605452773199111 NW_003726232.1 92047 463012 5.030169369995763 2.451560078720457 NW_003726233.1 87753 439452 5.007828792178045 2.213906103926639 NW_003726234.1 96536 457656 4.740780641418746 2.9464535855944987 NW_003726235.1 86544 448419 5.1813990571270105 2.498008135692505 NW_003726236.1 85476 420854 4.923651083345033 2.224897403494899 NW_003726237.1 110512 522962 4.732173881569422 3.640815930101036 NW_003726238.1 83291 406099 4.87566483773757 2.26433701349269 NW_003726239.1 82459 421902 5.116506384991329 2.438577333781484 NW_003726240.1 81605 421126 5.160541633478341 2.585723224371973 NW_003726241.1 82380 418706 5.082617140082545 2.6819356573651216 NW_003726242.1 102198 487675 4.7718644200473594 3.5581095005609353 NW_003726243.1 82108 414493 5.048143908023579 2.460692541960948 NW_003726244.1 87041 430894 4.950471616824255 2.8823049355468116 NW_003726245.1 79722 403357 5.059544416848548 2.286053365191242 NW_003726246.1 230124 1122239 4.876670838330639 7.262230365663741 NW_003726247.1 78357 390407 4.982413823908521 2.362025233356387 NW_003726248.1 256406 1257783 4.905435130223162 7.897720988792366 NW_003726249.1 78050 389463 4.989916720051249 2.3054115852734367 NW_003726250.1 81930 406019 4.955681679482485 2.6003413125579775 NW_003726251.1 77100 384639 4.988832684824903 2.3905461043288154 NW_003726252.1 77130 383910 4.9774406845585375 2.2627339066807344 NW_003726253.1 79078 393863 4.980689951693265 2.5582183486836465 NW_003726254.1 90550 449250 4.961347321921591 3.4229079763351598 NW_003726255.1 82767 416010 5.026278589292834 2.823118801272107 NW_003726256.1 89070 411181 4.616380374985966 3.2770869660563298 NW_003726257.1 97802 482961 4.938150549068526 3.675302348475415 NW_003726258.1 79712 396574 4.97508530710558 2.8537982515843616 NW_003726259.1 79581 409254 5.142609416820598 2.78694561271322 NW_003726260.1 73720 368641 5.00055615843733 2.377901073306027 NW_003726261.1 97799 477507 4.882534586243213 3.8068352146720876 NW_003726262.1 73171 368913 5.041792513427451 2.278173568598334 NW_003726263.1 104732 510514 4.874479624183631 3.975627220483294 NW_003726264.1 78935 373976 4.73777158421486 2.804815578036883 NW_003726265.1 72992 371226 5.085845024112231 2.5159537377963836 NW_003726266.1 68721 340277 4.95157229958819 2.127110577961278 NW_003726267.1 73611 367157 4.987800736302998 2.761510146459806 NW_003726268.1 68272 341055 4.995532575580032 2.17624046934362 NW_003726269.1 79297 402559 5.0765981058552025 3.189372582183118 NW_003726270.1 84443 406036 4.808403301635423 3.4647385483026367 NW_003726271.1 80679 385261 4.775232712353897 3.3200213219235195 NW_003726272.1 68834 337665 4.90549728331929 2.461610735703033 NW_003726273.1 67496 335289 4.967538817115089 2.423305458456478 NW_003726274.1 66523 331819 4.9880342137305895 2.2967757468789114 NW_003726275.1 67057 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