BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_med_error_med_variance/alignment/5X_med_error_med_variance.sorted.bam outfile = results/5X_med_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 = 102 (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 = 12,051,025,587 bp number of sequenced bases = 12,042,959,311 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,353,252 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 365.6164 std insert size = 27,304.0146 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 31.6878 >>>>>>> ACTG content number of A's = 3,530,824,606 bp (29.32%) number of C's = 2,501,034,780 bp (20.77%) number of T's = 3,520,433,336 bp (29.23%) number of G's = 2,490,645,888 bp (20.68%) number of N's = 20,701 bp (0%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0168 number of mismatches = 194,890,727 number of insertions = 5,625,481 mapped reads with insertion percentage = 6.78% number of deletions = 5,667,067 mapped reads with deletion percentage = 6.82% homopolymer indels = 28.48% >>>>>>> Coverage mean coverageData = 4.9984X std coverageData = 2.334X There is a 98.41% of reference with a coverageData >= 1X There is a 94.91% of reference with a coverageData >= 2X There is a 86.54% of reference with a coverageData >= 3X There is a 72.82% 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 3.6% 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 0.12% 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% 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 613788270 5.003214451463633 2.3095713581283013 NC_006584.3 85426708 428322387 5.013916572788922 2.316390211312231 NC_006585.3 91889043 459709629 5.002877535681812 2.2954977244297803 NC_006586.3 88276631 441762933 5.0043021351823 2.2944735389009034 NC_006587.3 88915250 444637996 5.0006944365561585 2.3027125602825436 NC_006588.3 77573801 387980357 5.001435433078753 2.3185110771941977 NC_006589.3 80974532 404940810 5.000841622647476 2.3028983073373985 NC_006590.3 74330416 371719455 5.000906425708689 2.2975222304114324 NC_006591.3 61074082 305816017 5.007296171885154 2.321072740119196 NC_006592.3 69331447 346570744 4.998752499713442 2.315268331200632 NC_006593.3 74389097 371946362 5.000011789362089 2.2973615432459478 NC_006594.3 72498081 362314566 4.997574570284143 2.2906677187639417 NC_006595.3 63241923 316176641 4.999478605354869 2.3031550605778723 NC_006596.3 60966679 304799035 4.999436413454635 2.3010514028565416 NC_006597.3 64190966 320812834 4.997787913021904 2.3116167317387855 NC_006598.3 59632846 298549313 5.0064575653491366 2.3235664004125782 NC_006599.3 64289059 321502853 5.000895300085198 2.292709180569573 NC_006600.3 55844845 279222428 4.9999678215598955 2.317711812964516 NC_006601.3 53741614 268636175 4.998662209884504 2.2888830281615977 NC_006602.3 58134056 290493766 4.996963673066266 2.312670776335107 NC_006603.3 50858623 254243369 4.999021876781839 2.3005089598340462 NC_006604.3 61439934 306990739 4.996599426685582 2.290051668734362 NC_006605.3 52294480 261314082 4.9969725676591485 2.2874139638682136 NC_006606.3 47698779 238478158 4.999670075412203 2.305494509339477 NC_006607.3 51628933 258047574 4.998119445931605 2.3057858616348574 NC_006608.3 38964690 194888180 5.0016612476578155 2.3068431611715026 NC_006609.3 45876710 229210870 4.996235998614548 2.3000389198546873 NC_006610.3 41182112 205833770 4.998135355466956 2.3084229176813857 NC_006611.3 41845238 209080891 4.9965277052552555 2.295326663723124 NC_006612.3 40214260 200985494 4.997866279275063 2.2976795944894404 NC_006613.3 39895921 199393914 4.997852136312382 2.299188167538198 NC_006614.3 38810281 193946864 4.997306358075583 2.2849273298022035 NC_006615.3 31377067 156846167 4.998751699768497 2.308435713336814 NC_006616.3 42124431 210519111 4.997553818590451 2.30289789390178 NC_006617.3 26524999 132548627 4.997120904698243 2.3032595130437548 NC_006618.3 30810995 153986738 4.997785303590487 2.297536655440335 NC_006619.3 30902991 154422167 4.996997442739442 2.3020919698477815 NC_006620.3 23914537 119515076 4.997591046818092 2.3103183066626953 NC_006621.3 123869142 619000413 4.997212405007213 2.317568372832019 NW_003726127.1 2660953 13341841 5.013933353952512 2.456057597435253 NW_003726128.1 1881673 9398372 4.994689300425738 2.8761820083164293 NW_003726129.1 1415205 7098963 5.016208252514653 2.741229824737632 NW_003726130.1 1067467 5339977 5.002475017963085 3.0793072304731375 NW_003726131.1 866315 4338617 5.008128682984826 2.2990836107314174 NW_003726132.1 881102 4458153 5.059746771656403 2.7178583726807046 NW_003726133.1 822601 4152635 5.048176454927723 2.671923275766846 NW_003726134.1 741967 3712835 5.004043306508241 2.301533583565621 NW_003726135.1 745551 3724470 4.995593862794094 3.2895500570644507 NW_003726136.1 602611 3026813 5.02283064862739 2.3601591234237924 NW_003726137.1 573630 2869397 5.002173875146 2.4009588191256985 NW_003726138.1 666183 3307748 4.965224270208036 3.1948611582102635 NW_003726139.1 557017 2803897 5.033772757384424 2.6488032016813716 NW_003726140.1 510604 2578182 5.049278893232329 2.3038975970956277 NW_003726141.1 497093 2494885 5.018950176325155 2.4186679927759753 NW_003726142.1 492630 2455178 4.983817469500436 2.5279350590238576 NW_003726143.1 577062 2886417 5.001918338064194 3.4972794199138213 NW_003726144.1 561270 2789269 4.969567231457231 3.419539223001387 NW_003726145.1 407330 2054326 5.043394790464734 2.3029297390344845 NW_003726146.1 405216 2038912 5.031667061517807 2.2570079033418784 NW_003726147.1 508668 2520821 4.955729473841484 3.4486983645259546 NW_003726148.1 540093 2710514 5.018606054883141 4.05887905318957 NW_003726149.1 448434 2235266 4.984604200395153 3.2579111563980963 NW_003726150.1 377800 1890265 5.003348332451032 2.5153542000421645 NW_003726151.1 384880 1928642 5.011021617127416 2.6961070454479827 NW_003726152.1 367143 1847014 5.03077547440643 2.4407646100362697 NW_003726153.1 399987 2016118 5.040458814911485 3.045343341422864 NW_003726154.1 376204 1890978 5.026469681343101 2.7465057208722063 NW_003726155.1 416178 2081695 5.001934268510109 3.30442423801598 NW_003726156.1 365470 1819034 4.977245738364298 2.923135700835947 NW_003726157.1 322752 1628137 5.044545037675986 2.304628868615377 NW_003726158.1 320591 1638936 5.112233344042721 2.426961205132459 NW_003726159.1 310270 1548917 4.992158442646727 2.4683254553656875 NW_003726160.1 433650 2132361 4.917239709443099 4.052863299108203 NW_003726161.1 273228 1381961 5.057904021549768 2.2544411300969815 NW_003726162.1 281659 1416146 5.027874131485236 2.4877343987579903 NW_003726163.1 320442 1601962 4.999226068992204 3.204403998777093 NW_003726164.1 265648 1346738 5.069633499969885 2.350962224350048 NW_003726165.1 241365 1238812 5.132525428293249 2.4280546508103797 NW_003726166.1 234529 1191401 5.079973052373054 2.343429815571965 NW_003726167.1 252720 1297435 5.133883349161127 2.8711831576083897 NW_003726168.1 254975 1282226 5.028830277478185 3.020902353312658 NW_003726169.1 226053 1137051 5.030019508699287 2.3415903758807497 NW_003726170.1 223744 1134338 5.069802989130435 2.358549252463193 NW_003726171.1 227140 1149405 5.060337236946377 2.483546778792114 NW_003726172.1 219672 1093405 4.977443643249936 2.3353928224707903 NW_003726173.1 214597 1081354 5.038998681249039 2.325740871778417 NW_003726174.1 386314 1924566 4.981869670785941 5.191917123060288 NW_003726175.1 204342 1024105 5.011720546926232 2.343904560433574 NW_003726176.1 201724 1017235 5.042706866808114 2.2727477915103615 NW_003726177.1 216332 1084133 5.011431503429914 2.690787398803226 NW_003726178.1 200877 1008871 5.022332073856141 2.2771999066594866 NW_003726179.1 310654 1510834 4.863397863861402 4.332574097742462 NW_003726180.1 200932 1001629 4.984915294726574 2.4355891440762867 NW_003726181.1 201410 1003788 4.983804180527283 2.4067216260342708 NW_003726182.1 292533 1419198 4.851411635610342 4.1090017595048405 NW_003726183.1 192561 970247 5.038647493521533 2.2988916570116515 NW_003726184.1 210134 1089730 5.185881389970209 2.8783724587407535 NW_003726185.1 197844 998039 5.044575524150341 2.6803246156731486 NW_003726186.1 196813 1002212 5.092204275124103 2.8221380490093195 NW_003726187.1 180359 902886 5.006049046623678 2.1970209083609826 NW_003726188.1 210247 1006800 4.788653345826575 3.1610642949264816 NW_003726189.1 177735 924342 5.200675162460967 2.5129756888937473 NW_003726190.1 172100 876103 5.090662405578152 2.357219245863349 NW_003726191.1 166866 847952 5.081634365299102 2.452324592104035 NW_003726192.1 164926 835112 5.06355577653008 2.4825219601467228 NW_003726193.1 157598 791060 5.019479942638866 2.812687588016825 NW_003726194.1 143980 719533 4.9974510348659535 2.4830234417206074 NW_003726195.1 141074 703456 4.986432652366843 2.231318016352688 NW_003726196.1 139526 696924 4.994940011180712 2.309138170316247 NW_003726197.1 142260 717856 5.046084633769155 2.478390036457315 NW_003726198.1 138160 704090 5.096192819918935 2.2860576087163063 NW_003726199.1 142296 717396 5.041575307809074 2.4872140144616366 NW_003726200.1 133119 667953 5.017713474410114 2.288994922885219 NW_003726201.1 129748 647812 4.992847673952585 2.2177083864276725 NW_003726202.1 125962 657576 5.2204315587240595 2.4027493899603454 NW_003726203.1 127429 640306 5.0248059703835075 2.372363565438213 NW_003726204.1 128261 639838 4.9885623845128295 2.449733240341109 NW_003726205.1 131872 653142 4.952848216452318 2.723686535986454 NW_003726206.1 133432 667744 5.004376761196714 2.872182339233438 NW_003726207.1 119670 610708 5.103267318459096 2.233418198921463 NW_003726208.1 144750 704274 4.8654507772020725 3.3972183166705534 NW_003726209.1 120779 610671 5.056102468144297 2.539268469224495 NW_003726210.1 115952 583189 5.029572581757969 2.3111480621289306 NW_003726211.1 118237 566801 4.793770139634801 2.5947471418966535 NW_003726212.1 111908 557669 4.983280909318369 2.3727462704452704 NW_003726213.1 117332 625951 5.334870282616848 2.781039434838235 NW_003726214.1 111759 558816 5.000187904329852 2.3691088632031523 NW_003726215.1 108801 562242 5.167617944688009 2.3761485466889294 NW_003726216.1 112014 579209 5.170862570750085 2.6684939867264723 NW_003726217.1 106428 546108 5.1312436576840685 2.382572491352572 NW_003726218.1 104912 526645 5.0198737989934425 2.3616984617001453 NW_003726219.1 104646 523897 5.006373869999809 2.201451427789938 NW_003726220.1 103248 516116 4.9987990082132345 2.38243059158696 NW_003726221.1 129482 640494 4.9465871704175095 3.6465522078685035 NW_003726222.1 118473 590410 4.983498349834983 3.1712071268381394 NW_003726223.1 99993 505051 5.050863560449232 2.292947226609345 NW_003726224.1 109585 542552 4.950969567002783 2.8096378913251776 NW_003726225.1 124049 606661 4.890494885085732 3.3816780574965075 NW_003726226.1 99658 506485 5.082231230809368 2.377965057207853 NW_003726227.1 101741 508435 4.997346202612516 2.7026931928814197 NW_003726228.1 97365 486773 4.999465927181225 2.342085782124005 NW_003726229.1 94395 472933 5.010148842629377 2.4179191496358934 NW_003726230.1 102992 475821 4.619980192636321 2.792955419878221 NW_003726231.1 95509 472860 4.950947031169838 2.5271112838129044 NW_003726232.1 92047 464154 5.042576075265897 2.390910545853586 NW_003726233.1 87753 448028 5.105557644752886 2.35362333154877 NW_003726234.1 96536 463056 4.796718322698268 3.043706528970336 NW_003726235.1 86544 446224 5.156036235903124 2.369669007223383 NW_003726236.1 85476 429103 5.020157705086808 2.2555663742131475 NW_003726237.1 110512 550075 4.977513754162444 3.7954402280757016 NW_003726238.1 83291 415965 4.994117011441812 2.280771546950501 NW_003726239.1 82459 421635 5.113268412180599 2.255772096354741 NW_003726240.1 81605 422979 5.183248575454935 2.450885908747832 NW_003726241.1 82380 427233 5.186125273124545 2.571320494007795 NW_003726242.1 102198 486939 4.764662713556039 3.606547743216477 NW_003726243.1 82108 411988 5.017635309592245 2.3974201142629523 NW_003726244.1 87041 428281 4.920451281579945 2.69557339857141 NW_003726245.1 79722 412012 5.168109179398409 2.263561090237684 NW_003726246.1 230124 1131281 4.915962698371313 7.33300830183219 NW_003726247.1 78357 391364 4.994627155199918 2.3816536852260093 NW_003726248.1 256406 1258416 4.907903871204262 7.916952446462596 NW_003726249.1 78050 391057 5.010339525944907 2.3827862552681434 NW_003726250.1 81930 411847 5.026815574270719 2.647483536662657 NW_003726251.1 77100 393402 5.102490272373541 2.340005297796089 NW_003726252.1 77130 379015 4.913976403474654 2.3594546887492913 NW_003726253.1 79078 400934 5.070107994638206 2.591095714808598 NW_003726254.1 90550 436701 4.822760905577029 3.315652913391779 NW_003726255.1 82767 421878 5.097176410888397 3.0053955133867 NW_003726256.1 89070 399250 4.482429549792299 3.026806342643244 NW_003726257.1 97802 487016 4.979611868877937 3.63007553354176 NW_003726258.1 79712 398484 4.999046567643517 2.897917528605276 NW_003726259.1 79581 410022 5.15225996154861 2.8879155777338013 NW_003726260.1 73720 370450 5.025094953879544 2.35874106330561 NW_003726261.1 97799 478748 4.89522387754476 3.737206087562927 NW_003726262.1 73171 370013 5.056825791638764 2.307704468250993 NW_003726263.1 104732 516418 4.930852079593629 4.010332106050579 NW_003726264.1 78935 381181 4.829049217710775 2.8204293296497704 NW_003726265.1 72992 382962 5.24662976764577 2.4607129110325303 NW_003726266.1 68721 341544 4.970009167503383 2.1789789188046442 NW_003726267.1 73611 368748 5.0094143538329865 2.791338106441408 NW_003726268.1 68272 341889 5.007748418092336 2.275581680573255 NW_003726269.1 79297 398166 5.021198784317187 3.3405814755466112 NW_003726270.1 84443 418732 4.958753241831769 3.4043502083291384 NW_003726271.1 80679 386860 4.795051996182402 3.249697766036574 NW_003726272.1 68834 344136 4.999506058052707 2.4363910401304922 NW_003726273.1 67496 337590 5.001629726205997 2.445463140412578 NW_003726274.1 66523 334104 5.022383235873307 2.289296874938706 NW_003726275.1 67057 334376 4.986444368224048 2.331035391438426 NW_003726276.1 66195 326640 4.934511670065715 2.493583270873851 NW_003726277.1 87584 437616 4.996529046401169 3.7074331586311966 NW_003726278.1 84679 380968 4.498966685955195 3.3179422048540195 NW_003726279.1 65840 329308 5.001640340218712 2.3111303152370164 NW_003726280.1 65696 334770 5.09574403312226 2.2977129922416237 NW_003726281.1 66021 332389 5.034595053089169 2.3783307231833937 NW_003726282.1 67300 339469 5.044115898959881 2.5937306041423693 NW_003726283.1 88153 397292 4.506846051750933 3.756866373774821 NW_003726284.1 92437 446606 4.831463591419021 4.006940695338712 NW_003726285.1 70351 347639 4.941493368964194 2.9630043685344702 NW_003726286.1 64646 339302 5.248615536924172 2.576066970998764 NW_003726287.1 69126 343536 4.9697074906692125 2.9172303469686227 NW_003726288.1 227674 1027454 4.512829747797289 7.788527175293659 NW_003726289.1 64123 320643 5.0004366607925395 2.408272814943368 NW_003726290.1 61944 305469 4.931373498643937 2.256342726294086 NW_003726291.1 62414 315503 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