BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_hi_error_low_variance/alignment/1X_hi_error_low_variance.sorted.bam outfile = results/1X_hi_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 = 16,073,030 (100%) number of supplementary alignments = 322 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,036,518 number of mapped paired reads (second in pair) = 8,036,512 number of mapped paired reads (both in pair) = 16,072,990 number of mapped paired reads (singletons) = 40 number of mapped bases = 2,403,072,255 bp number of sequenced bases = 2,402,892,311 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,998 duplication rate = 0.34% >>>>>>> Insert size mean insert size = 507.3839 std insert size = 78,351.7275 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.515 >>>>>>> ACTG content number of A's = 705,184,362 bp (29.35%) number of C's = 506,544,940 bp (21.08%) number of T's = 694,949,100 bp (28.92%) number of G's = 496,210,189 bp (20.65%) number of N's = 3,720 bp (0%) GC percentage = 41.73% >>>>>>> Mismatches and indels general error rate = 0.0496 number of mismatches = 118,996,885 number of insertions = 123,750 mapped reads with insertion percentage = 0.77% number of deletions = 122,069 mapped reads with deletion percentage = 0.76% homopolymer indels = 27.56% >>>>>>> Coverage mean coverageData = 0.9967X std coverageData = 1.0192X There is a 62.27% of reference with a coverageData >= 1X There is a 26.38% of reference with a coverageData >= 2X There is a 8.34% of reference with a coverageData >= 3X There is a 2.11% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.02% 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 122359738 0.9973993302917045 1.017430655119674 NC_006584.3 85426708 85391901 0.9995925513131092 1.019683005181559 NC_006585.3 91889043 91654794 0.9974507406720952 1.0145764571332383 NC_006586.3 88276631 88052692 0.9974632131124261 1.017238476571338 NC_006587.3 88915250 88652600 0.9970460635267854 1.0160065156960731 NC_006588.3 77573801 77332952 0.9968952275524052 1.0158882192286427 NC_006589.3 80974532 80752236 0.9972547417748583 1.0165822889194651 NC_006590.3 74330416 74112768 0.9970718850813374 1.0170259428369361 NC_006591.3 61074082 60997166 0.9987406114430013 1.018227887655754 NC_006592.3 69331447 69116990 0.9969067860360682 1.0175476791153413 NC_006593.3 74389097 74186736 0.997279695437088 1.0157010838087708 NC_006594.3 72498081 72261569 0.9967376791669837 1.0159075666361794 NC_006595.3 63241923 63046258 0.9969060871219871 1.0151330750570273 NC_006596.3 60966679 60796482 0.9972083603241698 1.0167755840393475 NC_006597.3 64190966 63974633 0.996629852867458 1.0183546225921851 NC_006598.3 59632846 59536584 0.9983857553939317 1.0195788210190935 NC_006599.3 64289059 64120555 0.9973789630363076 1.0153587447842969 NC_006600.3 55844845 55671790 0.9969011463815505 1.0186182355333677 NC_006601.3 53741614 53578019 0.9969558971563451 1.0141145241263596 NC_006602.3 58134056 57928815 0.9964695220990601 1.0173292921573789 NC_006603.3 50858623 50708726 0.9970526728574621 1.0151857655991479 NC_006604.3 61439934 61233159 0.996634517869111 1.015132951232922 NC_006605.3 52294480 52100613 0.996292782718176 1.015077610833229 NC_006606.3 47698779 47557281 0.9970335089709529 1.0145727267545963 NC_006607.3 51628933 51440453 0.9963493338124961 1.0158367400296164 NC_006608.3 38964690 38875462 0.9977100292598248 1.0161961002021582 NC_006609.3 45876710 45711985 0.996409398145595 1.0170045026017016 NC_006610.3 41182112 41038236 0.996506347221823 1.0154573136231524 NC_006611.3 41845238 41697719 0.9964746526235554 1.0142934368636953 NC_006612.3 40214260 40078947 0.9966351985589191 1.0161367483871946 NC_006613.3 39895921 39750643 0.9963585751034548 1.012557202345264 NC_006614.3 38810281 38675645 0.9965309192169982 1.0126853815475014 NC_006615.3 31377067 31283190 0.9970081014901744 1.016456830222179 NC_006616.3 42124431 41965281 0.9962219074246962 1.0160272283423104 NC_006617.3 26524999 26441232 0.9968419602956441 1.021145410683703 NC_006618.3 30810995 30707408 0.9966379858878299 1.0166433898390226 NC_006619.3 30902991 30791322 0.9963864662808852 1.014867378678179 NC_006620.3 23914537 23847825 0.9972103996828373 1.0164451482217391 NC_006621.3 123869142 123477463 0.9968379614674331 1.0189382280677726 NW_003726127.1 2660953 2668338 1.0027753214731714 1.0361250417821664 NW_003726128.1 1881673 1876928 0.99747830786752 1.0539384176057978 NW_003726129.1 1415205 1411248 0.9972039386519974 1.0414267307988103 NW_003726130.1 1067467 1072265 1.0044947525309915 1.0897522529184402 NW_003726131.1 866315 868932 1.0030208411490047 1.0191901138580424 NW_003726132.1 881102 887254 1.0069821655154567 1.0710252189618374 NW_003726133.1 822601 814622 0.9903002792362275 1.0387154002638448 NW_003726134.1 741967 742342 1.00050541331353 1.0116335748768728 NW_003726135.1 745551 739172 0.9914439119523681 1.1145701705478106 NW_003726136.1 602611 607080 1.0074160611074143 1.0351568064428225 NW_003726137.1 573630 571099 0.9955877482000592 1.0164316993690294 NW_003726138.1 666183 659474 0.9899291936299786 1.102780583141162 NW_003726139.1 557017 559502 1.0044612641983997 1.0449286289082769 NW_003726140.1 510604 517848 1.0141871195681977 1.0262360861384903 NW_003726141.1 497093 507428 1.0207908781656552 1.049452156619189 NW_003726142.1 492630 486950 0.9884700485151128 1.032511445093867 NW_003726143.1 577062 576530 0.9990780886629166 1.1511792169797463 NW_003726144.1 561270 552354 0.9841145972526592 1.1389869325885587 NW_003726145.1 407330 413505 1.015159698524538 1.0328712561899833 NW_003726146.1 405216 408884 1.0090519624101713 1.044550341740201 NW_003726147.1 508668 501187 0.985292961224217 1.1315295735556867 NW_003726148.1 540093 534137 0.9889722695906076 1.2024332986827069 NW_003726149.1 448434 449533 1.0024507508351286 1.1486121566078726 NW_003726150.1 377800 376015 0.995275277924828 1.035501750823604 NW_003726151.1 384880 382927 0.9949256911245064 1.0659087153376148 NW_003726152.1 367143 367642 1.001359143440022 1.0552633718192166 NW_003726153.1 399987 403653 1.0091652978721808 1.0903917239197438 NW_003726154.1 376204 375454 0.9980064007825541 1.067171044996155 NW_003726155.1 416178 411017 0.9875990561730797 1.1244144671289018 NW_003726156.1 365470 360202 0.9855856841874846 1.0497233821041085 NW_003726157.1 322752 325190 1.0075537874281182 1.0181766966299468 NW_003726158.1 320591 332689 1.0377365552994313 1.0674554310188835 NW_003726159.1 310270 307734 0.9918264737164405 1.0097868967491317 NW_003726160.1 433650 417313 0.9623267612129598 1.1759336536316194 NW_003726161.1 273228 273138 0.999670604769643 0.9971355669493506 NW_003726162.1 281659 281803 1.0005112565194083 1.0371567958458143 NW_003726163.1 320442 321281 1.0026182585304049 1.1015111878827997 NW_003726164.1 265648 270962 1.0200039149551285 1.0406138878006506 NW_003726165.1 241365 246270 1.0203219190852029 1.0483193467447713 NW_003726166.1 234529 228398 0.9738582435434424 0.9978451917285917 NW_003726167.1 252720 255079 1.0093344412788858 1.0838856484932868 NW_003726168.1 254975 259673 1.018425335817237 1.0924967812881432 NW_003726169.1 226053 217037 0.9601155481236701 1.0174467840686923 NW_003726170.1 223744 235630 1.053123212242563 1.037432876027787 NW_003726171.1 227140 228836 1.0074667605881835 1.043749885450813 NW_003726172.1 219672 220253 1.0026448523252849 1.0133884843737697 NW_003726173.1 214597 218535 1.0183506759181162 1.039337113380715 NW_003726174.1 386314 382901 0.9911652179315272 1.3648360270684226 NW_003726175.1 204342 205127 1.0038415988881386 1.0269418389939264 NW_003726176.1 201724 202504 1.0038666693105431 1.0352305774142183 NW_003726177.1 216332 218562 1.0103082299428656 1.0664822759933992 NW_003726178.1 200877 200872 0.9999751091463931 1.0137031096355744 NW_003726179.1 310654 302003 0.9721522980550709 1.246023469268354 NW_003726180.1 200932 199835 0.9945404415424124 1.062442746954564 NW_003726181.1 201410 206161 1.0235886996673451 1.020155877227953 NW_003726182.1 292533 272033 0.9299224361012262 1.1663139624712373 NW_003726183.1 192561 195651 1.0160468630719617 1.020776742554532 NW_003726184.1 210134 211719 1.0075428060190164 1.0675087461193742 NW_003726185.1 197844 198081 1.0011979135076121 1.0597501702694923 NW_003726186.1 196813 208797 1.0608902867188652 1.0912682691742466 NW_003726187.1 180359 181286 1.0051397490560494 0.9922809565445706 NW_003726188.1 210247 197538 0.939552050683244 1.0513357417672686 NW_003726189.1 177735 184071 1.0356485779390665 1.0389157681145753 NW_003726190.1 172100 178242 1.0356885531667634 0.9754862914758377 NW_003726191.1 166866 166764 0.9993887310776312 1.034898312152571 NW_003726192.1 164926 171024 1.0369741581072724 1.0383937819466433 NW_003726193.1 157598 158861 1.0080140610921458 1.052782483676969 NW_003726194.1 143980 143636 0.9976107792748993 1.0581809716132935 NW_003726195.1 141074 139432 0.9883607184881693 1.0246258244377309 NW_003726196.1 139526 137333 0.9842824993191234 0.9809254211135423 NW_003726197.1 142260 141666 0.9958245466048081 1.027826910245462 NW_003726198.1 138160 139651 1.0107918355529821 1.0248337060294008 NW_003726199.1 142296 143761 1.0102954404902458 1.0099378567240629 NW_003726200.1 133119 132460 0.9950495421389884 1.0195675642054203 NW_003726201.1 129748 130349 1.0046320559854487 1.0091883704834468 NW_003726202.1 125962 133772 1.0620028262491863 1.047050027991677 NW_003726203.1 127429 128776 1.0105705922513712 1.0318894439250301 NW_003726204.1 128261 127001 0.9901762811766632 1.0544034044820365 NW_003726205.1 131872 132850 1.0074162824557147 1.0822388382718018 NW_003726206.1 133432 138535 1.0382441992925235 1.1078840342377205 NW_003726207.1 119670 122216 1.0212751733934988 1.030475077299717 NW_003726208.1 144750 135412 0.9354887737478411 1.0725605756856476 NW_003726209.1 120779 120590 0.9984351584298595 1.0765217545354464 NW_003726210.1 115952 118498 1.0219573616668967 1.056129361933185 NW_003726211.1 118237 121698 1.0292717169752277 1.1041615831890998 NW_003726212.1 111908 112342 1.0038781856525003 0.967607580207112 NW_003726213.1 117332 122239 1.0418214979715679 1.0783250097011101 NW_003726214.1 111759 111481 0.9975125045857605 1.0010029000714564 NW_003726215.1 108801 109531 1.006709497155357 1.0186821610517764 NW_003726216.1 112014 118388 1.0569036013355473 1.0817912804228713 NW_003726217.1 106428 116198 1.0917991505994662 1.0626848353888745 NW_003726218.1 104912 107200 1.0218087540033551 1.0099650264646949 NW_003726219.1 104646 104636 0.9999044397301378 1.0503720862519075 NW_003726220.1 103248 103461 1.0020629939562995 0.9716088284603361 NW_003726221.1 129482 123529 0.9540244976135679 1.1416829765070815 NW_003726222.1 118473 116499 0.9833379757413081 1.1047987575331015 NW_003726223.1 99993 100424 1.0043103017211206 0.971101589608801 NW_003726224.1 109585 108298 0.9882556919286398 1.0518632362356222 NW_003726225.1 124049 121457 0.9791050310764294 1.1059795437723248 NW_003726226.1 99658 99843 1.001856348712597 1.0356861824634505 NW_003726227.1 101741 101562 0.9982406306208903 1.0712365577599687 NW_003726228.1 97365 98180 1.0083705643711807 1.0186534354251338 NW_003726229.1 94395 94620 1.002383600826315 1.0440761879368803 NW_003726230.1 102992 94241 0.9150322355134379 1.0444428262058683 NW_003726231.1 95509 91221 0.9551037075040049 1.0132377994307513 NW_003726232.1 92047 90522 0.9834323769378687 1.0326272544891295 NW_003726233.1 87753 83954 0.9567080327738083 0.9426907895888371 NW_003726234.1 96536 98878 1.0242603795475262 1.1337470253384812 NW_003726235.1 86544 84619 0.9777569791088926 1.0123387805478834 NW_003726236.1 85476 85921 1.0052061397351304 1.0248428831260088 NW_003726237.1 110512 103805 0.9393097582163022 1.1369889378961422 NW_003726238.1 83291 82148 0.9862770287305952 0.9812510442530916 NW_003726239.1 82459 86653 1.050861640330346 1.0320316154208395 NW_003726240.1 81605 88810 1.088291158629986 1.0622489342243557 NW_003726241.1 82380 84214 1.022262685117747 1.043146716020456 NW_003726242.1 102198 97525 0.9542750347364919 1.100742583837964 NW_003726243.1 82108 82640 1.0064792712037804 1.0169658354847821 NW_003726244.1 87041 82455 0.9473121862110959 1.0678938539156206 NW_003726245.1 79722 76926 0.9649281252351923 1.0221435486336503 NW_003726246.1 230124 223896 0.9729363299786202 1.742505855579422 NW_003726247.1 78357 77656 0.9910537667343058 1.0394274377612385 NW_003726248.1 256406 251185 0.9796377619868489 1.8230226311003654 NW_003726249.1 78050 77980 0.9991031390134529 1.0437447934635509 NW_003726250.1 81930 81852 0.9990479677773709 1.0363579117925106 NW_003726251.1 77100 78372 1.0164980544747082 0.9717437455047936 NW_003726252.1 77130 76813 0.9958900557500324 0.9536831314524011 NW_003726253.1 79078 80107 1.013012468701788 1.0274855237963099 NW_003726254.1 90550 87028 0.9611043622308117 1.0753930989748464 NW_003726255.1 82767 84011 1.0150301448644992 1.0763297736006532 NW_003726256.1 89070 81874 0.9192096104187718 1.0460220269831286 NW_003726257.1 97802 97225 0.994100325146725 1.2302364883408217 NW_003726258.1 79712 79591 0.9984820353271778 1.0643722913210616 NW_003726259.1 79581 82302 1.0341915783918272 1.075378185826264 NW_003726260.1 73720 74134 1.005615843733044 0.9847639416795767 NW_003726261.1 97799 94972 0.971093773964969 1.1522196185757463 NW_003726262.1 73171 75329 1.0294925585272854 0.9561323026295805 NW_003726263.1 104732 103967 0.9926956422105947 1.1389337085196203 NW_003726264.1 78935 73864 0.9357572686387534 1.0483993546877488 NW_003726265.1 72992 79145 1.0842969092503287 1.098353781457774 NW_003726266.1 68721 70968 1.0326974287335748 0.9943505752445939 NW_003726267.1 73611 71349 0.9692708970126748 1.1185100259284895 NW_003726268.1 68272 67899 0.9945365596437779 0.9935041207707158 NW_003726269.1 79297 78657 0.9919290767620464 1.0829195987378588 NW_003726270.1 84443 87266 1.033430835001125 1.2383658499341954 NW_003726271.1 80679 77264 0.9576717609291141 1.087302422485248 NW_003726272.1 68834 67302 0.9777435569631286 1.0027551181603442 NW_003726273.1 67496 67041 0.9932588597842835 1.0355321430432565 NW_003726274.1 66523 67671 1.0172571892428184 1.0570607042643327 NW_003726275.1 67057 67283 1.0033702670862101 1.039794886317839 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