BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_no_error_low_variance/alignment/1X_no_error_low_variance.sorted.bam outfile = results/1X_no_error_low_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 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 = 2,410,940,131 bp number of sequenced bases = 2,410,779,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,720 duplication rate = 0.34% >>>>>>> Insert size mean insert size = 360.5229 std insert size = 30,050.7223 median insert size = 350 >>>>>>> Mapping quality mean mapping quality = 32.447 >>>>>>> ACTG content number of A's = 707,491,642 bp (29.35%) number of C's = 497,844,243 bp (20.65%) number of T's = 707,590,113 bp (29.35%) number of G's = 497,849,156 bp (20.65%) number of N's = 3,989 bp (0%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0007 number of mismatches = 1,532,536 number of insertions = 112,992 mapped reads with insertion percentage = 0.7% number of deletions = 113,643 mapped reads with deletion percentage = 0.7% homopolymer indels = 28.9% >>>>>>> Coverage mean coverageData = 1X std coverageData = 1.0197X There is a 62.42% of reference with a coverageData >= 1X There is a 26.51% of reference with a coverageData >= 2X There is a 8.4% 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 122754394 1.0006163168309827 1.0179699976910657 NC_006584.3 85426708 85676182 1.00292032791431 1.0207653229009872 NC_006585.3 91889043 91939568 1.0005498479290942 1.0152052642183782 NC_006586.3 88276631 88318880 1.0004785977842765 1.0175085476372483 NC_006587.3 88915250 88944373 1.0003275366149227 1.0174539146392052 NC_006588.3 77573801 77592011 1.0002347442018473 1.0171906541353934 NC_006589.3 80974532 80994553 1.0002472505799724 1.0173958434090404 NC_006590.3 74330416 74332741 1.0000312792545114 1.0172707697005572 NC_006591.3 61074082 61182401 1.0017735673865715 1.0195813912600689 NC_006592.3 69331447 69331064 0.9999944758112433 1.0183285376024511 NC_006593.3 74389097 74421176 1.0004312325501141 1.0163625653795358 NC_006594.3 72498081 72502273 1.0000578222201495 1.0161304133667792 NC_006595.3 63241923 63251654 1.0001538694514396 1.0160623315674182 NC_006596.3 60966679 60981687 1.0002461672547394 1.0174735093368474 NC_006597.3 64190966 64193747 1.0000433238533908 1.0192882429138477 NC_006598.3 59632846 59750922 1.001980049719579 1.0206428394065186 NC_006599.3 64289059 64335258 1.0007186137224375 1.0165865547178428 NC_006600.3 55844845 55869304 1.0004379813391908 1.0189152555320033 NC_006601.3 53741614 53750719 1.0001694217817871 1.014731102788832 NC_006602.3 58134056 58128297 0.9999009358645129 1.0186578106640531 NC_006603.3 50858623 50866939 1.0001635120950876 1.0158247172339006 NC_006604.3 61439934 61438112 0.9999703450202274 1.0158467291481696 NC_006605.3 52294480 52282888 0.999778332244627 1.0157879747776464 NC_006606.3 47698779 47707247 1.0001775307497913 1.0157792958592924 NC_006607.3 51628933 51627973 0.9999814057749363 1.0172637645416347 NC_006608.3 38964690 39006965 1.0010849566620446 1.0176097882804807 NC_006609.3 45876710 45856645 0.9995626321067923 1.016887534543266 NC_006610.3 41182112 41172543 0.9997676418343965 1.0161606595431425 NC_006611.3 41845238 41838025 0.9998276267421397 1.0150485764521102 NC_006612.3 40214260 40211603 0.9999339289097947 1.0171730222402102 NC_006613.3 39895921 39887626 0.9997920840077862 1.0145844859992534 NC_006614.3 38810281 38794504 0.9995934840049213 1.0138871062419006 NC_006615.3 31377067 31386105 1.0002880447684928 1.0175957015829693 NC_006616.3 42124431 42117768 0.9998418257566494 1.0166104748101075 NC_006617.3 26524999 26526380 1.0000520640924435 1.0225165157192375 NC_006618.3 30810995 30803419 0.9997541137506271 1.0178680723754217 NC_006619.3 30902991 30902291 0.9999773484708973 1.0165603214182803 NC_006620.3 23914537 23918647 1.0001718619933975 1.017568262679555 NC_006621.3 123869142 123874302 1.0000416568639832 1.017777450809283 NW_003726127.1 2660953 2676625 1.0058896192454359 1.0324265096179737 NW_003726128.1 1881673 1879807 0.9990083292899457 1.055646802061033 NW_003726129.1 1415205 1417509 1.0016280326878437 1.0342585076373825 NW_003726130.1 1067467 1068298 1.000778478397927 1.0874439761072328 NW_003726131.1 866315 873260 1.0080167144745271 1.0228855836842248 NW_003726132.1 881102 885874 1.0054159450324707 1.0613757024607062 NW_003726133.1 822601 837010 1.0175163900846218 1.05617513849448 NW_003726134.1 741967 742502 1.000721056327303 1.0081067756937299 NW_003726135.1 745551 746701 1.001542483344533 1.1277545888046223 NW_003726136.1 602611 602098 0.9991487045540157 1.0244067221439428 NW_003726137.1 573630 574210 1.0010111047190697 1.0227538150793931 NW_003726138.1 666183 669271 1.0046353629558245 1.1065365704590566 NW_003726139.1 557017 561626 1.0082744332758247 1.0448035321900702 NW_003726140.1 510604 514178 1.006999553470008 1.018731850620219 NW_003726141.1 497093 508484 1.022915229142233 1.0424548460120366 NW_003726142.1 492630 487476 0.9895377869800864 1.0328580347992007 NW_003726143.1 577062 575705 0.9976484329240186 1.1514939209930208 NW_003726144.1 561270 556202 0.9909704776667201 1.1372952736188533 NW_003726145.1 407330 414877 1.0185279748606781 1.0298180809821758 NW_003726146.1 405216 412942 1.0190663744768222 1.048458206330617 NW_003726147.1 508668 508793 1.0002457398538929 1.1485173906158466 NW_003726148.1 540093 533722 0.9882038834052654 1.1980425997448716 NW_003726149.1 448434 450289 1.00413661765165 1.1212385891879553 NW_003726150.1 377800 373192 0.987803070407623 1.034810131942967 NW_003726151.1 384880 380377 0.9883002494283932 1.0605764087249314 NW_003726152.1 367143 368393 1.003404667935927 1.0498465902290637 NW_003726153.1 399987 402885 1.0072452354701529 1.0861317379035316 NW_003726154.1 376204 373479 0.9927565895099467 1.0722732864300208 NW_003726155.1 416178 414876 0.9968715309314764 1.1252941615767047 NW_003726156.1 365470 364943 0.9985580211782089 1.0594010730187433 NW_003726157.1 322752 328789 1.0187047640293476 1.029649617459163 NW_003726158.1 320591 327582 1.0218066009339002 1.0554456722168468 NW_003726159.1 310270 310188 0.9997357140555001 1.0101939067253831 NW_003726160.1 433650 426875 0.9843768015680848 1.204763436817092 NW_003726161.1 273228 274506 1.0046774122710702 1.0009277322327326 NW_003726162.1 281659 292491 1.038457851515485 1.0678157799050794 NW_003726163.1 320442 320985 1.0016945344243264 1.0928578215828348 NW_003726164.1 265648 267883 1.0084133891465399 1.03345961430751 NW_003726165.1 241365 244191 1.011708408427071 1.0545558819127543 NW_003726166.1 234529 237000 1.0105360104720524 1.0019298646983081 NW_003726167.1 252720 261599 1.035133744855967 1.0946117091643646 NW_003726168.1 254975 257095 1.0083145406412393 1.0916157539632159 NW_003726169.1 226053 224700 0.9940146779737495 1.0214415567720407 NW_003726170.1 223744 226495 1.0122953017734553 1.004560607277882 NW_003726171.1 227140 227997 1.0037730034340056 1.0407007309726737 NW_003726172.1 219672 221997 1.0105839615426635 1.0108813060380366 NW_003726173.1 214597 219892 1.0246741566750701 1.042063266160208 NW_003726174.1 386314 386417 1.000266622488442 1.373443239108083 NW_003726175.1 204342 205196 1.004179268089771 1.0204222531392988 NW_003726176.1 201724 205198 1.0172215502369575 1.0374082835590923 NW_003726177.1 216332 220504 1.019285172789971 1.0650422302196785 NW_003726178.1 200877 202505 1.0081044619344175 1.0223028102520701 NW_003726179.1 310654 304499 0.980186960412549 1.25050755414521 NW_003726180.1 200932 201895 1.0047926661756217 1.0589929119985542 NW_003726181.1 201410 205811 1.021850950796882 1.041234807114782 NW_003726182.1 292533 273902 0.9363114588781437 1.1625798762669308 NW_003726183.1 192561 192593 1.0001661811062468 1.0142344010035709 NW_003726184.1 210134 214505 1.0208010126871425 1.0767601120351047 NW_003726185.1 197844 197390 0.9977052627322537 1.0776378639700452 NW_003726186.1 196813 203398 1.033458155711259 1.063714088033632 NW_003726187.1 180359 182994 1.0146097505530636 1.008614757207712 NW_003726188.1 210247 203100 0.966006649321988 1.0650898039004206 NW_003726189.1 177735 182993 1.0295833684980449 1.0074386240256832 NW_003726190.1 172100 182696 1.0615688553166764 1.0170970015896241 NW_003726191.1 166866 172224 1.0321095969220813 1.0312722998922792 NW_003726192.1 164926 172515 1.04601457623419 1.0464547105458708 NW_003726193.1 157598 158077 1.0030393786723182 1.0295558535080307 NW_003726194.1 143980 143999 1.0001319627726073 1.0591644853396713 NW_003726195.1 141074 142194 1.007939095793697 1.0474624660061738 NW_003726196.1 139526 140994 1.010521336525092 1.0049962696185761 NW_003726197.1 142260 141898 0.9974553634190918 1.0243384615191875 NW_003726198.1 138160 138314 1.0011146496815286 1.019060071872937 NW_003726199.1 142296 148203 1.0415120593692022 1.042685702820066 NW_003726200.1 133119 132610 0.9961763534882323 1.0216408582116618 NW_003726201.1 129748 129287 0.9964469587199802 1.0097649081319724 NW_003726202.1 125962 124192 0.9859481430907734 1.0028737854402774 NW_003726203.1 127429 128095 1.0052264398213908 1.033373987271981 NW_003726204.1 128261 129314 1.0082098221595028 1.0664220901443573 NW_003726205.1 131872 131981 1.0008265590876 1.0921364880744064 NW_003726206.1 133432 138903 1.041002158402782 1.1034379110732233 NW_003726207.1 119670 121202 1.0128018718141556 1.0202861765042983 NW_003726208.1 144750 135903 0.938880829015544 1.087926626626084 NW_003726209.1 120779 120303 0.9960589175270536 1.0659731881642864 NW_003726210.1 115952 120913 1.0427849454946874 1.0597783959373197 NW_003726211.1 118237 116997 0.9895125891218485 1.0352217188753787 NW_003726212.1 111908 111618 0.9974085856239053 0.9767426075723333 NW_003726213.1 117332 118211 1.0074915624041183 1.0507108046725486 NW_003726214.1 111759 111890 1.0011721651052712 1.0026801319601155 NW_003726215.1 108801 108006 0.9926930818650563 1.0224771651869484 NW_003726216.1 112014 118212 1.0553323691681398 1.066982816125577 NW_003726217.1 106428 111600 1.04859623407374 1.0402241317229348 NW_003726218.1 104912 106788 1.0178816531950587 1.0076838675420536 NW_003726219.1 104646 101400 0.9689811364027292 1.0160827806110122 NW_003726220.1 103248 105579 1.022576708507671 0.9805186971745901 NW_003726221.1 129482 126911 0.9801439582335769 1.1542044471964101 NW_003726222.1 118473 118786 1.0026419521747572 1.1141693781263464 NW_003726223.1 99993 102295 1.023021611512806 0.9784681001872123 NW_003726224.1 109585 107704 0.9828352420495505 1.0525777487598702 NW_003726225.1 124049 120599 0.9721884094188586 1.0797835849464779 NW_003726226.1 99658 100223 1.0056693893114452 1.0248917901543872 NW_003726227.1 101741 101398 0.9966286944299741 1.0670589869488474 NW_003726228.1 97365 100805 1.0353309710881733 1.013664649344864 NW_003726229.1 94395 95397 1.0106149690131894 1.06511651753969 NW_003726230.1 102992 96304 0.935062917508156 1.0330583734213892 NW_003726231.1 95509 92696 0.9705472782669696 1.0154078719773676 NW_003726232.1 92047 93299 1.0136017469336318 1.041164894726009 NW_003726233.1 87753 89098 1.0153271113238294 1.017529557046846 NW_003726234.1 96536 94798 0.981996353691887 1.0846741825394641 NW_003726235.1 86544 86702 1.0018256609354779 1.0312008186159538 NW_003726236.1 85476 86095 1.0072417988675184 1.0348558086048392 NW_003726237.1 110512 103489 0.9364503402345447 1.1433997930458377 NW_003726238.1 83291 82808 0.9942010541355009 0.999261572812112 NW_003726239.1 82459 84602 1.025988673158782 1.031710293222189 NW_003726240.1 81605 84894 1.0403039029471233 1.0026644270285252 NW_003726241.1 82380 83098 1.0087157076960427 1.015064931399242 NW_003726242.1 102198 100503 0.9834145482299067 1.1870155604018 NW_003726243.1 82108 82198 1.0010961173089101 1.0120211068965732 NW_003726244.1 87041 87011 0.9996553348422008 1.0854665522377167 NW_003726245.1 79722 78913 0.9898522365219137 1.057896186226539 NW_003726246.1 230124 225600 0.9803410335297492 1.7523036316166334 NW_003726247.1 78357 78300 0.9992725602052146 1.0516781528478418 NW_003726248.1 256406 252633 0.9852850557319252 1.8244194346719973 NW_003726249.1 78050 79799 1.0224087123638692 1.0584215002332404 NW_003726250.1 81930 83403 1.0179787623581107 1.0611923691313896 NW_003726251.1 77100 77402 1.003916990920882 0.977874020187699 NW_003726252.1 77130 78000 1.0112796577207313 0.9620936220456886 NW_003726253.1 79078 76497 0.9673613394370115 0.9910665564308323 NW_003726254.1 90550 90885 1.0036996134732192 1.0867396099464848 NW_003726255.1 82767 84292 1.018425217780033 1.0794047928759223 NW_003726256.1 89070 76802 0.8622656337711913 1.0129592539043764 NW_003726257.1 97802 97187 0.9937117850350708 1.2277303273241764 NW_003726258.1 79712 79785 1.0009157968687274 1.0664220191968035 NW_003726259.1 79581 84286 1.0591221522725274 1.0904328994043562 NW_003726260.1 73720 73787 1.0009088442756375 0.983256105561896 NW_003726261.1 97799 95390 0.9753678462969969 1.1406941703272777 NW_003726262.1 73171 73808 1.008705634746006 0.9572360224645138 NW_003726263.1 104732 99302 0.9481533819653974 1.1110292333199667 NW_003726264.1 78935 73200 0.9273452840945081 1.0548145506177997 NW_003726265.1 72992 73796 1.011014905743095 1.039314891892205 NW_003726266.1 68721 70801 1.0302673127573814 1.004466282279091 NW_003726267.1 73611 69303 0.9414761380771896 1.071299465911656 NW_003726268.1 68272 68405 1.0019480899929694 0.9962855815169868 NW_003726269.1 79297 79195 0.9987136966089512 1.0877595248822194 NW_003726270.1 84443 84307 0.9983894461352628 1.1494329106990357 NW_003726271.1 80679 77995 0.9667323591021207 1.1112111665446434 NW_003726272.1 68834 67190 0.9761164540779266 0.9974153767477474 NW_003726273.1 67496 67500 1.000059262771127 1.0402587249480644 NW_003726274.1 66523 68092 1.0235858274581724 1.0425178513479212 NW_003726275.1 67057 67490 1.0064571931341992 1.040024038078866 NW_003726276.1 66195 65701 0.9925372006949166 1.0521222492930333 NW_003726277.1 87584 84297 0.9624703142126416 1.153299670600522 NW_003726278.1 84679 82201 0.9707365462511367 1.1511820279255849 NW_003726279.1 65840 67496 1.0251518833535844 1.0588356961129037 NW_003726280.1 65696 66903 1.0183725036531905 1.0157149641344438 NW_003726281.1 66021 66600 1.0087699368382788 1.0976192710556272 NW_003726282.1 67300 66003 0.9807280832095097 1.0386710924780274 NW_003726283.1 88153 78903 0.895068800834912 1.116675629602809 NW_003726284.1 92437 90306 0.9769464608327834 1.2244091890519713 NW_003726285.1 70351 69297 0.9850179812653693 1.0945020668653347 NW_003726286.1 64646 67197 1.0394610648764038 1.1172424688608864 NW_003726287.1 69126 67496 0.9764198709602755 1.011373676857935 NW_003726288.1 227674 207295 0.9104904380825215 1.7881158445653154 NW_003726289.1 64123 63301 0.9871808867333094 1.038754075671401 NW_003726290.1 61944 62702 1.0122368590985407 0.9724159394508306 NW_003726291.1 62414 63602 1.0190341910468805 1.0132162025391938 NW_003726292.1 61779 62707 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1.0240433776516067 NW_003729326.1 3257 3301 1.013509364445809 1.006035304084889 NW_003729327.1 3231 3900 1.2070566388115134 1.210763538779753 NW_003729328.1 3135 2098 0.6692185007974482 0.7927058993394166 NW_003729329.1 3134 1800 0.574345883854499 0.8507246449503002 NW_003729330.1 3059 3299 1.078457012095456 0.892592434632526 NW_003729331.1 3011 2100 0.697442710063102 0.8254041629233528 NW_003729332.1 2997 3600 1.2012012012012012 1.4699385285910411 NW_003729333.1 2955 2701 0.9140439932318105 1.1054388325961877 NW_003729334.1 2933 2700 0.9205591544493692 0.9837566348440178 NW_003729335.1 2850 2700 0.9473684210526315 1.1141994629388836 NW_003729336.1 2823 3900 1.381509032943677 0.9626600683511785 NW_003729337.1 2809 2997 1.066927732289071 0.9781190284755846 NW_003729338.1 2772 2399 0.8654401154401155 0.8970870695416379 NW_003729339.1 2729 2697 0.9882740930743862 0.9454961164303228 NW_003729340.1 2708 2100 0.7754800590841949 0.6964490743176198 NW_003729341.1 2700 1800 0.6666666666666666 0.90267093384844 NW_003729342.1 2641 2400 0.9087466868610374 0.9510965296349505 NW_003729343.1 2494 2703 1.0838011226944668 0.9028575263840277 NW_003729344.1 2361 2700 1.1435832274459974 0.8886133866360867 NW_003729345.1 2327 3001 1.2896433175762785 1.0390650012132752 NW_003729346.1 2250 1500 0.6666666666666666 0.6713171133426189 NW_003729347.1 2145 1800 0.8391608391608392 0.9817710293567153 NW_003729348.1 2046 2100 1.0263929618768328 0.791133286407234 NW_003729349.1 1999 1500 0.7503751875937968 0.804078279923525 NW_003729350.1 1819 1500 0.8246289169873557 0.6710279563120027 NW_003729351.1 1790 1500 0.8379888268156425 0.5568350105061994 NW_003729352.1 1685 1800 1.0682492581602374 1.0275583503576122 NW_003729353.1 1573 2400 1.5257469802924348 1.5069677640524686 NW_003729354.1 1115 1500 1.345291479820628 0.7717331146460592 NC_002008.4 16727 16801 1.0044239851736714 1.0359324608459846