BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_no_error_med_variance/alignment/1X_no_error_med_variance.sorted.bam outfile = results/1X_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 = 16,073,088 number of mapped reads = 16,073,088 (100%) number of supplementary alignments = 4 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,036,544 number of mapped paired reads (second in pair) = 8,036,544 number of mapped paired reads (both in pair) = 16,073,088 number of mapped paired reads (singletons) = 0 number of mapped bases = 2,410,687,090 bp number of sequenced bases = 2,409,074,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,523 duplication rate = 0.34% >>>>>>> Insert size mean insert size = 363.276 std insert size = 25,032.0883 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 32.129 >>>>>>> ACTG content number of A's = 706,237,463 bp (29.32%) number of C's = 498,249,483 bp (20.68%) number of T's = 706,353,663 bp (29.32%) number of G's = 498,230,169 bp (20.68%) number of N's = 4,206 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 15,284,034 number of insertions = 1,129,030 mapped reads with insertion percentage = 6.8% number of deletions = 1,135,318 mapped reads with deletion percentage = 6.83% homopolymer indels = 28.66% >>>>>>> Coverage mean coverageData = 0.9999X std coverageData = 1.0194X There is a 62.39% of reference with a coverageData >= 1X There is a 26.48% of reference with a coverageData >= 2X There is a 8.39% of reference with a coverageData >= 3X There is a 2.12% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% 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 122767419 1.0007224884074293 1.0170265988939382 NC_006584.3 85426708 85680823 1.0029746551862915 1.019146177413111 NC_006585.3 91889043 91968127 1.0008606466823253 1.0161725465006741 NC_006586.3 88276631 88384529 1.0012222713845977 1.0172033753859733 NC_006587.3 88915250 88956416 1.0004629801974352 1.0181539064309664 NC_006588.3 77573801 77608652 1.0004492625029422 1.0190336098259816 NC_006589.3 80974532 80985886 1.0001402169264775 1.018187238221541 NC_006590.3 74330416 74341006 1.0001424719592582 1.0160702757260567 NC_006591.3 61074082 61185558 1.001825258707941 1.0189147691145548 NC_006592.3 69331447 69312525 0.9997270791131765 1.0161897762102141 NC_006593.3 74389097 74378698 0.9998602080087086 1.016416576750096 NC_006594.3 72498081 72470474 0.9996192037138196 1.0174344821709642 NC_006595.3 63241923 63240270 0.9999738622748711 1.017693067301387 NC_006596.3 60966679 60961934 0.9999221706007637 1.0158349463341874 NC_006597.3 64190966 64181978 0.9998599802969159 1.0166697401663225 NC_006598.3 59632846 59717811 1.001424802029405 1.016660310560011 NC_006599.3 64289059 64325524 1.0005672038223488 1.0180127356701396 NC_006600.3 55844845 55854982 1.0001815207831628 1.01834873305174 NC_006601.3 53741614 53742509 1.0000166537610873 1.0184724069165538 NC_006602.3 58134056 58113979 0.9996546430546667 1.0173104201556191 NC_006603.3 50858623 50854492 0.9999187748358818 1.0175791867890476 NC_006604.3 61439934 61415434 0.9996012365508075 1.0145910161024252 NC_006605.3 52294480 52274998 0.9996274558997431 1.017458554942526 NC_006606.3 47698779 47711096 1.0002582246392513 1.0189996157474122 NC_006607.3 51628933 51613440 0.9996999163240503 1.017530465395228 NC_006608.3 38964690 38992825 1.000722064002049 1.018156967926389 NC_006609.3 45876710 45861629 0.9996712711090224 1.0156966289319842 NC_006610.3 41182112 41174140 0.9998064208071699 1.016423091954908 NC_006611.3 41845238 41835759 0.999773474821675 1.013695458606468 NC_006612.3 40214260 40194544 0.9995097261518675 1.0152251378074584 NC_006613.3 39895921 39891921 0.9998997391237064 1.0168602207194812 NC_006614.3 38810281 38796781 0.9996521540258881 1.0105555916571491 NC_006615.3 31377067 31388642 1.0003688999994804 1.0141304984795743 NC_006616.3 42124431 42105994 0.9995623204975754 1.0176412181476222 NC_006617.3 26524999 26513266 0.9995576625657931 1.0162539603691059 NC_006618.3 30810995 30803018 0.9997410989161499 1.0154820399220397 NC_006619.3 30902991 30884324 0.9993959484374829 1.0183615070280645 NC_006620.3 23914537 23909864 0.9998045958405969 1.015636940914926 NC_006621.3 123869142 123850702 0.99985113322251 1.0167952309744726 NW_003726127.1 2660953 2663807 1.001072548068305 1.028838834253713 NW_003726128.1 1881673 1900905 1.0102206919055543 1.0774218422977087 NW_003726129.1 1415205 1419752 1.0032129620796988 1.0664656576602576 NW_003726130.1 1067467 1065427 0.9980889338967855 1.0848336260506244 NW_003726131.1 866315 865295 0.9988225991700479 1.012559381530785 NW_003726132.1 881102 871998 0.9896674845818078 1.0375087667159364 NW_003726133.1 822601 831858 1.0112533293783985 1.0529750138990641 NW_003726134.1 741967 741313 0.9991185591812035 1.024313692721856 NW_003726135.1 745551 743775 0.997617869200095 1.1210751126382688 NW_003726136.1 602611 605044 1.0040374304484982 1.0084977494151652 NW_003726137.1 573630 569584 0.9929466729424891 1.0183142869526887 NW_003726138.1 666183 659599 0.9901168297599908 1.1211757904870399 NW_003726139.1 557017 558591 1.0028257665385436 1.0645095344375168 NW_003726140.1 510604 520105 1.0186073747953404 1.044296634752038 NW_003726141.1 497093 495512 0.996819508623135 1.0471864083327782 NW_003726142.1 492630 486816 0.9881980390962791 1.0309167126991208 NW_003726143.1 577062 575046 0.9965064412489473 1.141016321194362 NW_003726144.1 561270 560859 0.9992677321075418 1.1243590613094996 NW_003726145.1 407330 405909 0.9965114280804261 1.0202768189662863 NW_003726146.1 405216 408514 1.0081388691463318 1.044420844469595 NW_003726147.1 508668 508684 1.0000314547012983 1.1523998368199468 NW_003726148.1 540093 538701 0.9974226660963945 1.222235133985535 NW_003726149.1 448434 443851 0.9897799899204788 1.1254016430692144 NW_003726150.1 377800 381850 1.01071995764955 1.0743785695531345 NW_003726151.1 384880 381246 0.9905580960299314 1.0552750719719546 NW_003726152.1 367143 375589 1.0230046603094707 1.0399337304579797 NW_003726153.1 399987 399537 0.9988749634363117 1.0801042690906462 NW_003726154.1 376204 374666 0.995911792538091 1.0621695991155005 NW_003726155.1 416178 410388 0.9860876836353676 1.1348154818195755 NW_003726156.1 365470 366528 1.0028949024543738 1.1019875473404042 NW_003726157.1 322752 332951 1.0316001140194329 1.0369918752303824 NW_003726158.1 320591 327258 1.0207959674476201 1.0270754280138472 NW_003726159.1 310270 310443 1.0005575788829084 1.0263303841059819 NW_003726160.1 433650 434042 1.0009039548022598 1.2153949164868356 NW_003726161.1 273228 278390 1.0188926464344796 1.0324019638739055 NW_003726162.1 281659 288284 1.023521350285274 1.040422756713812 NW_003726163.1 320442 326644 1.0193545165739821 1.113400913476769 NW_003726164.1 265648 265087 0.9978881828585195 0.9979789005795752 NW_003726165.1 241365 249526 1.0338118617032295 1.0797780536937374 NW_003726166.1 234529 236399 1.0079734275931762 1.0049995903704765 NW_003726167.1 252720 247450 0.9791468819246597 1.0741807028845833 NW_003726168.1 254975 258226 1.0127502696342778 1.072770507724596 NW_003726169.1 226053 223155 0.9871799976111797 1.007907989969163 NW_003726170.1 223744 224347 1.0026950443363845 1.0050535896928752 NW_003726171.1 227140 232111 1.0218851809456724 1.0413349422153535 NW_003726172.1 219672 217806 0.9915055173167268 1.006329284046745 NW_003726173.1 214597 214464 0.999380233647255 1.0230518026927582 NW_003726174.1 386314 386621 1.0007946903296283 1.4085252730525055 NW_003726175.1 204342 206687 1.0114758590989616 1.0202416790807012 NW_003726176.1 201724 208567 1.0339225872974955 1.0352926109590193 NW_003726177.1 216332 219303 1.0137335206996654 1.0792333336607605 NW_003726178.1 200877 202767 1.0094087426634208 1.0002332035523112 NW_003726179.1 310654 304740 0.9809627431161356 1.2355325892566238 NW_003726180.1 200932 200112 0.9959190173790138 1.0295546758458545 NW_003726181.1 201410 206960 1.027555732088774 1.0270226552918829 NW_003726182.1 292533 282889 0.9670327792078158 1.1871100211524659 NW_003726183.1 192561 190747 0.9905796085396316 0.9925618671953639 NW_003726184.1 210134 215937 1.0276157118790867 1.0863870075171285 NW_003726185.1 197844 196222 0.9918016214795495 1.060227770669975 NW_003726186.1 196813 210872 1.0714332894676672 1.1040858658143444 NW_003726187.1 180359 183293 1.0162675552647775 1.0702460268802654 NW_003726188.1 210247 202198 0.9617164573097357 1.074671315243008 NW_003726189.1 177735 187452 1.0546712802768166 1.0736753040647284 NW_003726190.1 172100 176402 1.0249970947123765 1.0353042082811217 NW_003726191.1 166866 169522 1.015916963311879 0.9898938849496575 NW_003726192.1 164926 169214 1.0259995391872718 0.9859353686085471 NW_003726193.1 157598 158380 1.0049619919034505 1.0719145287247331 NW_003726194.1 143980 143977 0.9999791637727462 1.0327495885481726 NW_003726195.1 141074 140367 0.9949884457802288 1.048640697507936 NW_003726196.1 139526 141257 1.0124062898671216 0.9812975848372492 NW_003726197.1 142260 143374 1.00783073246169 1.0472657200277529 NW_003726198.1 138160 139151 1.0071728430804865 0.9686897542420254 NW_003726199.1 142296 142748 1.0031764772024512 1.0311738206662469 NW_003726200.1 133119 132877 0.9981820776898865 1.006104420357608 NW_003726201.1 129748 130187 1.0033834818263094 1.0820211007778608 NW_003726202.1 125962 134966 1.0714818754862578 1.0365948715758309 NW_003726203.1 127429 128707 1.0100291142518578 1.0493298187001476 NW_003726204.1 128261 128697 1.003399318576964 1.0405620707818626 NW_003726205.1 131872 134391 1.0191018563455472 1.0709460750407438 NW_003726206.1 133432 133173 0.9980589363870735 1.0771480553762536 NW_003726207.1 119670 123279 1.0301579343193783 1.003241219439712 NW_003726208.1 144750 141327 0.9763523316062176 1.1051776071813233 NW_003726209.1 120779 122686 1.0157891686468674 1.0280936624774462 NW_003726210.1 115952 116631 1.00585587139506 1.009723038862772 NW_003726211.1 118237 113425 0.9593020797212378 1.0103562842504685 NW_003726212.1 111908 110063 0.983513243021053 1.0108890189609314 NW_003726213.1 117332 129435 1.1031517403606859 1.0639824628660894 NW_003726214.1 111759 111886 1.0011363738043468 1.0334556151210814 NW_003726215.1 108801 110967 1.0199079052582238 1.0261473858929013 NW_003726216.1 112014 115804 1.0338350563322443 1.0712967274904008 NW_003726217.1 106428 109806 1.0317397677302966 1.0531534417858612 NW_003726218.1 104912 108908 1.0380890651212444 1.064784840615736 NW_003726219.1 104646 101672 0.9715803757429811 1.00658404539433 NW_003726220.1 103248 101364 0.9817526731752673 1.0814455029872305 NW_003726221.1 129482 123611 0.9546577902720069 1.133807209009631 NW_003726222.1 118473 119949 1.012458534856043 1.115241782330393 NW_003726223.1 99993 101402 1.014090986369046 1.0219075944043885 NW_003726224.1 109585 109468 0.9989323356298764 1.0752654479191341 NW_003726225.1 124049 116716 0.940886262686519 1.1031992206181345 NW_003726226.1 99658 97800 0.9813562383351061 1.0468577299497477 NW_003726227.1 101741 102312 1.0056122900305677 1.0466580399034056 NW_003726228.1 97365 99879 1.0258203666615313 1.037146696000255 NW_003726229.1 94395 93138 0.9866836167169871 0.9933475629304794 NW_003726230.1 102992 100489 0.9756971415255554 1.0304752142159952 NW_003726231.1 95509 94468 0.9891005036174602 1.027314519419046 NW_003726232.1 92047 90604 0.9843232261779309 1.0036514347832148 NW_003726233.1 87753 89966 1.0252185110480554 1.0143103353681457 NW_003726234.1 96536 97765 1.0127310019060247 1.07978089034857 NW_003726235.1 86544 89984 1.0397485672028102 1.013363280447989 NW_003726236.1 85476 85427 0.9994267396696148 1.0023716839244783 NW_003726237.1 110512 113670 1.0285760822354133 1.1966259508315582 NW_003726238.1 83291 83706 1.0049825311258118 1.0606559541633944 NW_003726239.1 82459 83999 1.018675948046908 1.0463352633481495 NW_003726240.1 81605 83727 1.0260033086207954 1.0408044416984867 NW_003726241.1 82380 85776 1.04122359796067 1.0179434093557518 NW_003726242.1 102198 98656 0.9653417875105188 1.1172735168486858 NW_003726243.1 82108 83102 1.012106006722853 1.0432917357130653 NW_003726244.1 87041 89974 1.0336967635941683 1.1017118723649193 NW_003726245.1 79722 81956 1.0280223777627255 1.0566964290852312 NW_003726246.1 230124 224384 0.975056925831291 1.7134624056830148 NW_003726247.1 78357 77709 0.9917301581224396 1.0552832449865532 NW_003726248.1 256406 251120 0.9793842577786791 1.8282981882778202 NW_003726249.1 78050 79467 1.0181550288276746 1.061268608631122 NW_003726250.1 81930 79476 0.9700476016111315 1.0187477390991706 NW_003726251.1 77100 78596 1.0194033722438391 1.0701900247813765 NW_003726252.1 77130 76193 0.9878516789835343 1.0549691432560386 NW_003726253.1 79078 80684 1.0203090619388453 1.0369352740394935 NW_003726254.1 90550 84307 0.9310546659304252 1.0689343575930177 NW_003726255.1 82767 84016 1.0150905554145977 1.0660729881601652 NW_003726256.1 89070 82176 0.9226002020882452 1.011522013952763 NW_003726257.1 97802 96541 0.9871066031369502 1.127150442853453 NW_003726258.1 79712 79768 1.0007025291047773 1.041516050034858 NW_003726259.1 79581 81865 1.0287003179150802 1.1921556948169578 NW_003726260.1 73720 76187 1.0334644601193705 1.0744811547568256 NW_003726261.1 97799 100437 1.026973690937535 1.2139175109039353 NW_003726262.1 73171 73201 1.0004099984966721 0.9800879350136558 NW_003726263.1 104732 99895 0.9538154527747011 1.2203800017363409 NW_003726264.1 78935 73496 0.9310952049154367 1.0372370288253827 NW_003726265.1 72992 76233 1.0444021262604122 1.0636829150298963 NW_003726266.1 68721 70776 1.0299035229405857 0.9923981885687285 NW_003726267.1 73611 71699 0.974025621170749 1.0554107148680514 NW_003726268.1 68272 68393 1.0017723224748067 1.0332594914867956 NW_003726269.1 79297 79810 1.0064693494079222 1.1342993803752475 NW_003726270.1 84443 89421 1.0589510083725115 1.187417175557027 NW_003726271.1 80679 75879 0.9405049641170565 1.110334661245789 NW_003726272.1 68834 67494 0.9805328761949037 1.0169927922293285 NW_003726273.1 67496 67154 0.9949330330686262 1.01795175410326 NW_003726274.1 66523 66302 0.9966778407468094 0.99793070518894 NW_003726275.1 67057 68404 1.020087388341262 0.9938345045495145 NW_003726276.1 66195 66873 1.0102424654430093 1.0041892203896952 NW_003726277.1 87584 85747 0.9790258494702229 1.181300861209926 NW_003726278.1 84679 76779 0.9067065033833654 1.0795386070253472 NW_003726279.1 65840 65375 0.9929374240583232 0.9239974886019041 NW_003726280.1 65696 67491 1.0273228202630298 1.0430696131310733 NW_003726281.1 66021 65424 0.9909574226382515 1.028492513346575 NW_003726282.1 67300 65970 0.9802377414561664 1.064508108693125 NW_003726283.1 88153 83436 0.9464907603825168 1.187287071243563 NW_003726284.1 92437 91136 0.985925549293032 1.2143019431422997 NW_003726285.1 70351 69858 0.9929922815596083 1.097467734766008 NW_003726286.1 64646 65226 1.008971939485815 0.9842332042932511 NW_003726287.1 69126 69337 1.0030523970720133 1.0563210177806635 NW_003726288.1 227674 206715 0.9079429359522827 1.7827118201729388 NW_003726289.1 64123 66282 1.033669666110444 1.081849081330843 NW_003726290.1 61944 62079 1.0021793878341727 1.0226264162652756 NW_003726291.1 62414 61497 0.98530778351011 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