BamQC report ----------------------------------- >>>>>>> Input bam file = results/5X_no_error_hi_variance/alignment/5X_no_error_hi_variance.sorted.bam outfile = results/5X_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 = 80,365,277 (100%) number of supplementary alignments = 550 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 40,182,637 number of mapped paired reads (second in pair) = 40,182,640 number of mapped paired reads (both in pair) = 80,365,274 number of mapped paired reads (singletons) = 3 number of mapped bases = 12,031,492,099 bp number of sequenced bases = 11,992,168,373 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,489,437 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 407.5133 std insert size = 46,871.6158 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 30.9523 >>>>>>> ACTG content number of A's = 3,499,583,918 bp (29.18%) number of C's = 2,496,384,941 bp (20.82%) number of T's = 3,499,606,061 bp (29.18%) number of G's = 2,496,573,378 bp (20.82%) number of N's = 20,075 bp (0%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0345 number of mismatches = 376,196,093 number of insertions = 27,341,078 mapped reads with insertion percentage = 29.1% number of deletions = 27,432,721 mapped reads with deletion percentage = 29.1% homopolymer indels = 28.21% >>>>>>> Coverage mean coverageData = 4.9903X std coverageData = 2.3417X There is a 98.27% of reference with a coverageData >= 1X There is a 94.68% of reference with a coverageData >= 2X There is a 86.22% of reference with a coverageData >= 3X There is a 72.46% of reference with a coverageData >= 4X There is a 55.45% of reference with a coverageData >= 5X There is a 38.46% of reference with a coverageData >= 6X There is a 24.22% of reference with a coverageData >= 7X There is a 13.91% of reference with a coverageData >= 8X There is a 7.33% of reference with a coverageData >= 9X There is a 3.57% of reference with a coverageData >= 10X There is a 1.62% 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 612636087 4.993822583097803 2.313562725998614 NC_006584.3 85426708 427601748 5.005480815203601 2.3221030707236596 NC_006585.3 91889043 458948775 4.994597397210895 2.308485443711617 NC_006586.3 88276631 440843569 4.9938875555864835 2.3001119602030924 NC_006587.3 88915250 443840980 4.991730664874698 2.3131375138981647 NC_006588.3 77573801 387261981 4.992174883888956 2.324442027143506 NC_006589.3 80974532 404262160 4.992460592424295 2.3109458201512814 NC_006590.3 74330416 371136098 4.993058265676867 2.3065794130669093 NC_006591.3 61074082 305423286 5.000865768232096 2.3317120599366876 NC_006592.3 69331447 346034880 4.991023481739823 2.3165090906623447 NC_006593.3 74389097 371396024 4.992613689073279 2.3025466397618026 NC_006594.3 72498081 361747357 4.989750790783 2.2965729636665135 NC_006595.3 63241923 315688215 4.99175546891577 2.3102055218666693 NC_006596.3 60966679 304350648 4.992081789464045 2.3099335667274348 NC_006597.3 64190966 320306822 4.9899049969118705 2.3136883285827325 NC_006598.3 59632846 298078755 4.99856664563687 2.326981903033369 NC_006599.3 64289059 321005503 4.99315914703309 2.307848395505355 NC_006600.3 55844845 278846579 4.993237585313381 2.3244639291758533 NC_006601.3 53741614 268223287 4.990979374009869 2.2940244754257004 NC_006602.3 58134056 290086938 4.989965571987614 2.313171552830618 NC_006603.3 50858623 253848831 4.991264332893952 2.315997839757781 NC_006604.3 61439934 306572036 4.989784591891 2.301336020307729 NC_006605.3 52294480 260917343 4.9893859351885705 2.2988701507853 NC_006606.3 47698779 238078280 4.991286674235414 2.3118733470800055 NC_006607.3 51628933 257650207 4.990422850691104 2.3136587878917627 NC_006608.3 38964690 194613918 4.994622515924033 2.3168609447038095 NC_006609.3 45876710 228889520 4.989231355081914 2.306124970439316 NC_006610.3 41182112 205503934 4.99012614991674 2.315043996396515 NC_006611.3 41845238 208731299 4.9881733018223 2.3050417914261843 NC_006612.3 40214260 200675105 4.990147897785512 2.3079182432987477 NC_006613.3 39895921 199105905 4.990633127632271 2.305572754161335 NC_006614.3 38810281 193683088 4.990509808470596 2.2918099288840224 NC_006615.3 31377067 156573244 4.990053531772106 2.3118274991484817 NC_006616.3 42124431 210149720 4.988784774327278 2.310757079193947 NC_006617.3 26524999 132342565 4.989352308740898 2.3088564235255995 NC_006618.3 30810995 153706167 4.9886791062735885 2.3042080496531843 NC_006619.3 30902991 154215049 4.990295243589852 2.313638846610939 NC_006620.3 23914537 119345753 4.990510709030244 2.321189665695091 NC_006621.3 123869142 618113752 4.990054359139744 2.325896511407254 NW_003726127.1 2660953 13316347 5.004352575938019 2.4454963807309005 NW_003726128.1 1881673 9445078 5.0195108289272365 2.854391014198458 NW_003726129.1 1415205 7091697 5.011074014012104 2.7599774148277585 NW_003726130.1 1067467 5357816 5.019186541598007 3.0888861143481887 NW_003726131.1 866315 4359519 5.032256165482532 2.351854480612254 NW_003726132.1 881102 4465329 5.067891118167931 2.694232173048454 NW_003726133.1 822601 4145682 5.039723997417946 2.626379247706271 NW_003726134.1 741967 3693367 4.977804942807429 2.327588287464855 NW_003726135.1 745551 3745060 5.023211021110561 3.307297239947414 NW_003726136.1 602611 3014173 5.001855259860839 2.362053235359413 NW_003726137.1 573630 2869181 5.001797325802347 2.458941681888229 NW_003726138.1 666183 3324774 4.990781812204754 3.1987830703695823 NW_003726139.1 557017 2796473 5.020444618386872 2.6813212508821027 NW_003726140.1 510604 2553783 5.0014943087010675 2.346716524415699 NW_003726141.1 497093 2500467 5.030179463400208 2.4435348625904387 NW_003726142.1 492630 2467491 5.008811887217587 2.5788626337215494 NW_003726143.1 577062 2856685 4.950395278150355 3.5012991756584992 NW_003726144.1 561270 2764729 4.925844958754253 3.41297684432587 NW_003726145.1 407330 2040729 5.010013993567869 2.301652969464494 NW_003726146.1 405216 2052414 5.064987562189055 2.3440910801579085 NW_003726147.1 508668 2514529 4.94335991255593 3.4252502665492117 NW_003726148.1 540093 2708346 5.014591931389594 4.040239816308925 NW_003726149.1 448434 2230201 4.973309338720971 3.2562866610482573 NW_003726150.1 377800 1895518 5.017252514557967 2.5400653386301206 NW_003726151.1 384880 1930983 5.017104032425691 2.734928855342862 NW_003726152.1 367143 1832340 4.990807396572998 2.546772682047341 NW_003726153.1 399987 1998536 4.996502386327555 3.0335591638744543 NW_003726154.1 376204 1882570 5.004120105049388 2.6868753585878333 NW_003726155.1 416178 2063409 4.95799633810533 3.2482139616383856 NW_003726156.1 365470 1824429 4.992007551919446 2.9916007751300415 NW_003726157.1 322752 1616474 5.008408933174698 2.420458433613308 NW_003726158.1 320591 1623869 5.0652357676915445 2.41517333227533 NW_003726159.1 310270 1548025 4.98928352725046 2.45054752454993 NW_003726160.1 433650 2118442 4.885142395941427 4.051821855740435 NW_003726161.1 273228 1368793 5.009709839401525 2.2724466469130467 NW_003726162.1 281659 1421708 5.047621414547378 2.5865899025952066 NW_003726163.1 320442 1599242 4.990737793422834 3.168077495518012 NW_003726164.1 265648 1335443 5.027114828645425 2.401869713515107 NW_003726165.1 241365 1216219 5.038920307418225 2.4193077901921445 NW_003726166.1 234529 1183982 5.048339437766758 2.3401922062764977 NW_003726167.1 252720 1277942 5.056750553972776 2.8863408894528466 NW_003726168.1 254975 1277620 5.010765761349152 2.9908911919233723 NW_003726169.1 226053 1123926 4.971957903677456 2.44315027102669 NW_003726170.1 223744 1151685 5.147333559782608 2.4466918798506545 NW_003726171.1 227140 1146297 5.046654045962843 2.4833226938072914 NW_003726172.1 219672 1110263 5.054185330856914 2.3733194960978388 NW_003726173.1 214597 1083511 5.04905007991724 2.226472610083776 NW_003726174.1 386314 1921042 4.972747557686234 5.20589923681464 NW_003726175.1 204342 1021279 4.997890790928933 2.3238208798210587 NW_003726176.1 201724 1021618 5.064434573972358 2.3426955961069105 NW_003726177.1 216332 1098931 5.079835623023871 2.649301692541919 NW_003726178.1 200877 1004658 5.001359040606938 2.2939143896401415 NW_003726179.1 310654 1512518 4.868818685740406 4.333387741090435 NW_003726180.1 200932 1001358 4.983566579738419 2.408210353836499 NW_003726181.1 201410 1007751 5.003480462737699 2.4006317597576214 NW_003726182.1 292533 1421640 4.859759411758674 4.113753715494755 NW_003726183.1 192561 959046 4.980478913175565 2.319318755961775 NW_003726184.1 210134 1070701 5.095324887928655 2.831958995669882 NW_003726185.1 197844 990523 5.006585997048179 2.736234273450231 NW_003726186.1 196813 1014489 5.154583284640751 2.8212309727258984 NW_003726187.1 180359 908316 5.03615566730798 2.3525167078034546 NW_003726188.1 210247 1025212 4.876226533553392 3.2564510264142243 NW_003726189.1 177735 909505 5.117196950516218 2.4566326369150726 NW_003726190.1 172100 870011 5.055264381173736 2.319066310085545 NW_003726191.1 166866 844669 5.061959895964427 2.349196269700447 NW_003726192.1 164926 847246 5.137128166571674 2.3892509501848025 NW_003726193.1 157598 787450 4.99657356057818 2.8203820628965266 NW_003726194.1 143980 718453 4.989949993054591 2.4586114557634158 NW_003726195.1 141074 702063 4.976558401973432 2.3148297354758234 NW_003726196.1 139526 702857 5.037462551782464 2.3045660517370696 NW_003726197.1 142260 719528 5.05783776184451 2.593500529514586 NW_003726198.1 138160 704248 5.097336421540243 2.272091588799675 NW_003726199.1 142296 711011 4.996704053522235 2.5268676895145985 NW_003726200.1 133119 664577 4.992352706976464 2.387493636704576 NW_003726201.1 129748 650872 5.0164318525141045 2.253769668391645 NW_003726202.1 125962 659663 5.237000047633413 2.4160081917777316 NW_003726203.1 127429 636023 4.991195096877477 2.433073359177892 NW_003726204.1 128261 643891 5.020162013394563 2.508887445847022 NW_003726205.1 131872 662171 5.021316124727008 2.6891698416536007 NW_003726206.1 133432 693687 5.198805384015828 2.902368269147565 NW_003726207.1 119670 596450 4.9841230049302245 2.3687557083969266 NW_003726208.1 144750 695986 4.808193436960276 3.378129062700908 NW_003726209.1 120779 605970 5.017180138931437 2.5900951997263135 NW_003726210.1 115952 583654 5.033582861873879 2.301910692889059 NW_003726211.1 118237 575610 4.868273044816767 2.482002849210267 NW_003726212.1 111908 558297 4.98889266182936 2.2838404988979164 NW_003726213.1 117332 615226 5.243462993897658 2.841808902730833 NW_003726214.1 111759 557506 4.988466253277141 2.3534785726244 NW_003726215.1 108801 549193 5.047683385263003 2.4335635288581443 NW_003726216.1 112014 567447 5.065857839198672 2.6320634481456424 NW_003726217.1 106428 550235 5.17002104709287 2.4747731079780704 NW_003726218.1 104912 532220 5.0730135732804635 2.320296357048184 NW_003726219.1 104646 529446 5.059400263746345 2.3676185565062777 NW_003726220.1 103248 521582 5.051739501007283 2.4188923791752983 NW_003726221.1 129482 639934 4.942262244945243 3.6983965780334147 NW_003726222.1 118473 586548 4.950900205110025 3.176799450212229 NW_003726223.1 99993 499476 4.995109657676037 2.3045123492141837 NW_003726224.1 109585 550921 5.027339508144363 2.89372464215533 NW_003726225.1 124049 616311 4.968286725406895 3.4777176283575044 NW_003726226.1 99658 496237 4.979399546448855 2.3447070234017673 NW_003726227.1 101741 506061 4.974012443361084 2.6374720489294265 NW_003726228.1 97365 491318 5.0461459456683615 2.446248295925574 NW_003726229.1 94395 471219 4.991991101223582 2.2979940384552915 NW_003726230.1 102992 480549 4.665886670809384 2.8020785307286697 NW_003726231.1 95509 470081 4.921850296830665 2.6122322557553197 NW_003726232.1 92047 456612 4.960639673210425 2.513449583213771 NW_003726233.1 87753 446009 5.082549884334439 2.387133261995519 NW_003726234.1 96536 451519 4.677208502527554 2.9491312251670347 NW_003726235.1 86544 433704 5.011369938990572 2.296165450551584 NW_003726236.1 85476 425267 4.975279610650943 2.3966345722368696 NW_003726237.1 110512 531280 4.807441725785435 3.7418761451636247 NW_003726238.1 83291 413887 4.969168337515458 2.244433431392919 NW_003726239.1 82459 418240 5.07209643580446 2.3404180095093907 NW_003726240.1 81605 421013 5.159156914404755 2.343297262994693 NW_003726241.1 82380 429764 5.216848749696529 2.5103331881847004 NW_003726242.1 102198 475431 4.652057770210767 3.519185967763001 NW_003726243.1 82108 413447 5.0354045890778 2.39081546416324 NW_003726244.1 87041 424790 4.880343746050712 2.696103708207187 NW_003726245.1 79722 404297 5.0713353904819245 2.3838331241160624 NW_003726246.1 230124 1119621 4.865294363039057 7.277595634602149 NW_003726247.1 78357 392629 5.010771213803489 2.173191771597271 NW_003726248.1 256406 1256047 4.898664617832656 7.89180293775366 NW_003726249.1 78050 387491 4.964650864830237 2.2321107925982573 NW_003726250.1 81930 407325 4.971622116440864 2.5911022007422537 NW_003726251.1 77100 385378 4.998417639429313 2.3345739994640473 NW_003726252.1 77130 387799 5.027862051082588 2.4186278473094456 NW_003726253.1 79078 391084 4.945547434178912 2.511528608771141 NW_003726254.1 90550 423864 4.680993926007731 3.3225446890127004 NW_003726255.1 82767 411313 4.969528918530332 2.8969863026470866 NW_003726256.1 89070 384528 4.317143819467835 2.995700562322975 NW_003726257.1 97802 484511 4.953998895728104 3.7538961766525425 NW_003726258.1 79712 398296 4.996688077077479 2.739520823207264 NW_003726259.1 79581 404382 5.081388773702265 2.8468074698597854 NW_003726260.1 73720 368561 4.999470971242539 2.426998845968655 NW_003726261.1 97799 474466 4.851440198775038 3.822229430966461 NW_003726262.1 73171 376915 5.151152779106477 2.383797943181277 NW_003726263.1 104732 514534 4.9128633082534465 4.0211148180729355 NW_003726264.1 78935 372891 4.7240260974219295 2.7924494578889143 NW_003726265.1 72992 368439 5.047662757562472 2.7004809850144462 NW_003726266.1 68721 346031 5.0353021638218305 2.263969657378575 NW_003726267.1 73611 367271 4.989349417885914 2.7357033691592156 NW_003726268.1 68272 340484 4.987168971174127 2.2312194691469984 NW_003726269.1 79297 393119 4.957551988095388 3.224662490758035 NW_003726270.1 84443 418711 4.95850455336736 3.515576419561153 NW_003726271.1 80679 385598 4.779409759664845 3.25011498587416 NW_003726272.1 68834 342235 4.971888892117268 2.491572281729829 NW_003726273.1 67496 336955 4.992221761289558 2.4590219011807726 NW_003726274.1 66523 325875 4.898681658975091 2.2531344530198036 NW_003726275.1 67057 336172 5.013227552679064 2.3807891940661 NW_003726276.1 66195 328141 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