BamQC report ----------------------------------- >>>>>>> Input bam file = results/1X_haploid_hi_error_low_variance/alignment/1X_haploid_hi_error_low_variance.sorted.bam outfile = results/1X_haploid_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 = 16,073,041 (100%) number of supplementary alignments = 323 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,036,517 number of mapped paired reads (second in pair) = 8,036,524 number of mapped paired reads (both in pair) = 16,073,012 number of mapped paired reads (singletons) = 29 number of mapped bases = 2,402,913,438 bp number of sequenced bases = 2,402,653,010 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,877 duplication rate = 0.34% >>>>>>> Insert size mean insert size = 543.2154 std insert size = 86,988.1893 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.5424 >>>>>>> ACTG content number of A's = 705,130,445 bp (29.35%) number of C's = 506,493,600 bp (21.08%) number of T's = 694,860,862 bp (28.92%) number of G's = 496,164,210 bp (20.65%) number of N's = 3,893 bp (0%) GC percentage = 41.73% >>>>>>> Mismatches and indels general error rate = 0.0499 number of mismatches = 119,668,047 number of insertions = 179,206 mapped reads with insertion percentage = 1.11% number of deletions = 178,413 mapped reads with deletion percentage = 1.1% homopolymer indels = 27.52% >>>>>>> Coverage mean coverageData = 0.9967X std coverageData = 1.0189X There is a 62.28% of reference with a coverageData >= 1X There is a 26.37% 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 122350748 0.9973260494876925 1.01642273708106 NC_006584.3 85426708 85381220 0.9994675201577474 1.0176376514007193 NC_006585.3 91889043 91698418 0.9979254871551987 1.0165099145579077 NC_006586.3 88276631 88052877 0.9974653087972966 1.0167222668528613 NC_006587.3 88915250 88633766 0.9968342438445599 1.0150279163331783 NC_006588.3 77573801 77325897 0.9968042818992459 1.01650780453114 NC_006589.3 80974532 80745873 0.997176161512116 1.0180100636574805 NC_006590.3 74330416 74114249 0.997091809630125 1.0151720382252505 NC_006591.3 61074082 61013648 0.999010480419501 1.0183529245949368 NC_006592.3 69331447 69116034 0.9968929971993805 1.0168700345667183 NC_006593.3 74389097 74175423 0.9971276166989902 1.0161533643223122 NC_006594.3 72498081 72253715 0.9966293452650147 1.0171265676533665 NC_006595.3 63241923 63048537 0.9969421233443518 1.0149524387104667 NC_006596.3 60966679 60800454 0.9972735106663756 1.0152190339921372 NC_006597.3 64190966 63970969 0.9965727731843138 1.0156664473251378 NC_006598.3 59632846 59526621 0.9982186830392097 1.0196483786103316 NC_006599.3 64289059 64119960 0.9973697079622833 1.0153062057409166 NC_006600.3 55844845 55681804 0.9970804646337544 1.0175236429167775 NC_006601.3 53741614 53570942 0.996824211494653 1.0157838155182675 NC_006602.3 58134056 57908650 0.9961226514110765 1.0162245672416355 NC_006603.3 50858623 50677901 0.9964465809465585 1.0156703567804217 NC_006604.3 61439934 61230626 0.9965932906112822 1.0140730213387408 NC_006605.3 52294480 52106082 0.9963973635458274 1.0139650024900584 NC_006606.3 47698779 47559665 0.9970834892859627 1.0168785448127262 NC_006607.3 51628933 51443966 0.9964173770548386 1.0165984814829327 NC_006608.3 38964690 38878008 0.9977753704700333 1.0174417900856343 NC_006609.3 45876710 45705844 0.99627553937499 1.0173602136598323 NC_006610.3 41182112 41050716 0.9968093914173222 1.0131616564955395 NC_006611.3 41845238 41676688 0.9959720625797372 1.0122688243789189 NC_006612.3 40214260 40068268 0.9963696459912479 1.0147096793457298 NC_006613.3 39895921 39757196 0.9965228274840428 1.0138312998051702 NC_006614.3 38810281 38663288 0.9962125242020278 1.0121527661086218 NC_006615.3 31377067 31281793 0.996963578526954 1.0149866005227604 NC_006616.3 42124431 41984926 0.9966882638723358 1.0146960823601334 NC_006617.3 26524999 26438837 0.9967516681150488 1.0178286783633177 NC_006618.3 30810995 30698769 0.9963575989675114 1.012959821365556 NC_006619.3 30902991 30790390 0.9963563073878512 1.017364300721773 NC_006620.3 23914537 23845056 0.9970946123690373 1.0201615515775746 NC_006621.3 123869142 123482019 0.9968747422178802 1.0186802074832042 NW_003726127.1 2660953 2658444 0.99905710472902 1.027415023807326 NW_003726128.1 1881673 1863348 0.990261325958336 1.0714554760639703 NW_003726129.1 1415205 1423763 1.0060471804438227 1.0534401376315359 NW_003726130.1 1067467 1071461 1.0037415676550188 1.0949497237153123 NW_003726131.1 866315 868088 1.0020465996779462 1.0168272628503212 NW_003726132.1 881102 885764 1.0052911013707835 1.0584012719280542 NW_003726133.1 822601 833564 1.0133272388436192 1.0533038009294065 NW_003726134.1 741967 742563 1.0008032702263039 1.010785092045221 NW_003726135.1 745551 731780 0.9815290972716822 1.1151621867725936 NW_003726136.1 602611 608427 1.0096513339451154 1.02891694736131 NW_003726137.1 573630 573720 1.0001568955598557 1.0428488773790345 NW_003726138.1 666183 662781 0.9948932950855846 1.1102290801016925 NW_003726139.1 557017 561200 1.0075096451275276 1.0560575492291258 NW_003726140.1 510604 512872 1.0044417983407885 1.0007766009617027 NW_003726141.1 497093 489303 0.9843288881557375 1.0212156150356826 NW_003726142.1 492630 487462 0.9895093680855814 1.0318669975725627 NW_003726143.1 577062 571352 0.9901050493707781 1.1290659174718778 NW_003726144.1 561270 552327 0.9840664920626436 1.1306163440050871 NW_003726145.1 407330 407506 1.000432082095598 1.0191293397326322 NW_003726146.1 405216 417634 1.0306453841901604 1.0325946137237427 NW_003726147.1 508668 507154 0.9970235988896491 1.1342613842534734 NW_003726148.1 540093 528202 0.9779834213737264 1.2022149799826831 NW_003726149.1 448434 442924 0.9877127960859347 1.1230320113037748 NW_003726150.1 377800 374744 0.9919110640550556 1.0235857004737459 NW_003726151.1 384880 387134 1.005856370816878 1.0599757546961643 NW_003726152.1 367143 368920 1.0048400759377136 1.0384140633438954 NW_003726153.1 399987 402381 1.0059851945188218 1.1055463300965664 NW_003726154.1 376204 367567 0.9770417114118936 1.0430300007023143 NW_003726155.1 416178 411535 0.9888437159100193 1.0937731489619071 NW_003726156.1 365470 368062 1.007092237392946 1.0997809698355752 NW_003726157.1 322752 332245 1.0294126759865159 1.0419543309848114 NW_003726158.1 320591 326475 1.01835360318911 1.0310810772243937 NW_003726159.1 310270 307571 0.9913011248267638 1.0040732960181182 NW_003726160.1 433650 424668 0.9792874437910758 1.2096557250111044 NW_003726161.1 273228 274891 1.0060864918675978 1.0491725219105879 NW_003726162.1 281659 285848 1.014872594165285 1.0609631258872065 NW_003726163.1 320442 323071 1.0082042928205417 1.1249923950920726 NW_003726164.1 265648 268339 1.0101299463952298 1.0101343285364572 NW_003726165.1 241365 241572 1.0008576222733205 1.0218276873291314 NW_003726166.1 234529 235529 1.0042638650230888 1.0295155904393147 NW_003726167.1 252720 258223 1.0217750870528648 1.0730739195911818 NW_003726168.1 254975 256574 1.0062712030591234 1.105531664619209 NW_003726169.1 226053 222226 0.9830703419109678 1.0303215727074506 NW_003726170.1 223744 225699 1.0087376644736843 1.0760040630612118 NW_003726171.1 227140 230476 1.0146869771946816 1.0249192348329155 NW_003726172.1 219672 217603 0.9905814122874104 1.0085517191909592 NW_003726173.1 214597 212103 0.9883782159116856 1.002239805587066 NW_003726174.1 386314 387591 1.0033056011431116 1.3837359309235384 NW_003726175.1 204342 205392 1.0051384443726694 0.9998258422817682 NW_003726176.1 201724 197707 0.980086653050703 1.0192380504490153 NW_003726177.1 216332 211359 0.9770121849749459 1.039713228219412 NW_003726178.1 200877 201240 1.0018070759718634 1.0243102410812959 NW_003726179.1 310654 301248 0.9697219414525485 1.210500105256401 NW_003726180.1 200932 198465 0.9877222144805208 1.0243325502099665 NW_003726181.1 201410 203186 1.0088178342684078 1.0238784779600854 NW_003726182.1 292533 287579 0.9830651584607548 1.201657067862541 NW_003726183.1 192561 195086 1.0131127279147907 1.0169150859804759 NW_003726184.1 210134 220288 1.0483215472032132 1.105274527105037 NW_003726185.1 197844 197861 1.000085926285356 1.064547586719387 NW_003726186.1 196813 204228 1.0376753568107797 1.108905790582165 NW_003726187.1 180359 181467 1.0061433030788594 1.043364128922503 NW_003726188.1 210247 202194 0.9616974320679962 1.1134627743760017 NW_003726189.1 177735 173595 0.9767068950966327 0.9761377497144978 NW_003726190.1 172100 175293 1.0185531667635095 1.084142219547448 NW_003726191.1 166866 163501 0.9798341183944003 0.9963129408583069 NW_003726192.1 164926 166403 1.0089555315717351 1.0094417333247077 NW_003726193.1 157598 159280 1.0106727242731506 1.083684111373174 NW_003726194.1 143980 143593 0.9973121266842617 0.993344661246514 NW_003726195.1 141074 136439 0.9671449026751917 1.004087599875602 NW_003726196.1 139526 138587 0.9932700715278873 1.0047749487760143 NW_003726197.1 142260 145117 1.0200829467172783 1.0390760678494495 NW_003726198.1 138160 140481 1.0167993630573249 0.984968259102762 NW_003726199.1 142296 141092 0.991538764266037 1.0332373728635196 NW_003726200.1 133119 132739 0.9971454112485821 0.9640306622055217 NW_003726201.1 129748 129480 0.9979344575638931 0.9868822327816952 NW_003726202.1 125962 127898 1.0153697146758547 0.9866005867751921 NW_003726203.1 127429 128033 1.0047398943725525 1.03114929548047 NW_003726204.1 128261 130328 1.0161155768316168 1.0105757931251689 NW_003726205.1 131872 132116 1.001850279058481 1.0664482835215001 NW_003726206.1 133432 137259 1.0286812758558666 1.0713030897507831 NW_003726207.1 119670 123208 1.0295646360825603 1.0141924783929286 NW_003726208.1 144750 135171 0.9338238341968912 1.1269991865137603 NW_003726209.1 120779 119771 0.991654178292584 1.0322797052630788 NW_003726210.1 115952 115723 0.9980250448461432 0.9960702281033601 NW_003726211.1 118237 113940 0.9636577382714379 1.0452570686505893 NW_003726212.1 111908 111507 0.996416699431676 0.9929267136946457 NW_003726213.1 117332 124707 1.0628558279071354 1.0967627991906514 NW_003726214.1 111759 111513 0.9977988349931549 1.0173489323826856 NW_003726215.1 108801 109426 1.0057444324960247 1.0344100630016049 NW_003726216.1 112014 113686 1.0149267055903726 1.051987014034354 NW_003726217.1 106428 107886 1.013699402412899 1.0688871071037676 NW_003726218.1 104912 108224 1.031569315235626 1.0285312721862665 NW_003726219.1 104646 104258 0.9962922615293466 1.016865028057258 NW_003726220.1 103248 102255 0.990382380288238 1.018103790863282 NW_003726221.1 129482 130630 1.0088660972181462 1.1877098463149571 NW_003726222.1 118473 116316 0.9817933199969613 1.0757620878505896 NW_003726223.1 99993 102257 1.0226415849109438 1.0489743256187503 NW_003726224.1 109585 106948 0.9759364876579824 1.036657141616195 NW_003726225.1 124049 112840 0.909640545268402 1.0670189482472534 NW_003726226.1 99658 99530 0.9987156073772301 0.9955187298986247 NW_003726227.1 101741 101490 0.9975329513175613 1.0293954616698742 NW_003726228.1 97365 94520 0.970780054434345 0.9866175192450969 NW_003726229.1 94395 96805 1.0255310132951958 1.000268493785496 NW_003726230.1 102992 87314 0.8477745844337424 1.0086986859174663 NW_003726231.1 95509 93830 0.9824205048738862 1.0209576488135257 NW_003726232.1 92047 90286 0.9808684693689094 1.0113571664426202 NW_003726233.1 87753 88807 1.0120109853794172 1.0186933551500552 NW_003726234.1 96536 92667 0.9599216872462086 1.0798339808929995 NW_003726235.1 86544 89661 1.036016361619523 1.0132926905306963 NW_003726236.1 85476 84637 0.9901843792409565 0.9786051136693709 NW_003726237.1 110512 105336 0.9531634573620964 1.1579397739429076 NW_003726238.1 83291 83570 1.0033497016484374 1.0429314373346659 NW_003726239.1 82459 85581 1.0378612401314593 1.0479864397501533 NW_003726240.1 81605 86606 1.0612830096195085 1.0108716913079758 NW_003726241.1 82380 86885 1.0546856033017722 1.0490259318831312 NW_003726242.1 102198 95066 0.9302138985107341 1.1079853781847435 NW_003726243.1 82108 81109 0.9878330978710966 0.9618561083871983 NW_003726244.1 87041 90321 1.0376833905860456 1.0687242692839942 NW_003726245.1 79722 78717 0.987393693083465 0.9208745849948513 NW_003726246.1 230124 225224 0.9787071318071996 1.733096721695906 NW_003726247.1 78357 77154 0.9846471916995291 0.9999633352203973 NW_003726248.1 256406 252762 0.9857881640835238 1.8496186864840924 NW_003726249.1 78050 82215 1.0533632286995516 1.0183750776242706 NW_003726250.1 81930 81662 0.996728914927377 1.0995161309570287 NW_003726251.1 77100 79824 1.035330739299611 1.008315210365992 NW_003726252.1 77130 77493 1.0047063399455465 1.0639320044700205 NW_003726253.1 79078 79311 1.0029464579276157 1.0844679372858008 NW_003726254.1 90550 91788 1.013672004417449 1.1249508003456645 NW_003726255.1 82767 83420 1.00788961784286 1.0413654199524047 NW_003726256.1 89070 77140 0.8660604019310655 1.045773380529972 NW_003726257.1 97802 95831 0.9798470378928856 1.1647550774709392 NW_003726258.1 79712 79552 0.9979927739863509 1.0648898058653338 NW_003726259.1 79581 81818 1.0281097246830273 1.070964205491458 NW_003726260.1 73720 72882 0.9886326641345632 0.97909036696724 NW_003726261.1 97799 91533 0.9359298152332846 1.1384250558935474 NW_003726262.1 73171 74974 1.024640909649998 1.0420221732920072 NW_003726263.1 104732 101557 0.9696845281289386 1.1678961666308179 NW_003726264.1 78935 78377 0.9929308925064927 1.072461153631541 NW_003726265.1 72992 77811 1.0660209338009645 1.1267834843214086 NW_003726266.1 68721 69810 1.0158466844196097 1.0446040147292759 NW_003726267.1 73611 74123 1.0069554821969542 1.0646317186627774 NW_003726268.1 68272 67931 0.9950052730255449 1.000074456268444 NW_003726269.1 79297 81340 1.0257639002736547 1.1291768740994819 NW_003726270.1 84443 84813 1.0043816538967114 1.1414238680267943 NW_003726271.1 80679 76440 0.9474584464358755 1.0988577958714876 NW_003726272.1 68834 66267 0.9627073829793416 0.9636055424334014 NW_003726273.1 67496 67325 0.9974665165343132 0.9890540821885403 NW_003726274.1 66523 67571 1.0157539497617365 0.9725322081864379 NW_003726275.1 67057 67620 1.0083958423430812 0.9621000521492045 NW_003726276.1 66195 67273 1.0162852179167612 1.0450073185880009 NW_003726277.1 87584 86085 0.9828850018268177 1.2287468334396672 NW_003726278.1 84679 78067 0.9219168861228876 1.069462564834231 NW_003726279.1 65840 66639 1.0121354799513973 1.0018249007113302 NW_003726280.1 65696 65302 0.9940026790063322 1.0000183354789058 NW_003726281.1 66021 64736 0.9805364959634055 1.0461905329615204 NW_003726282.1 67300 69487 1.0324962852897475 1.0748199721898664 NW_003726283.1 88153 81001 0.9188683311968963 1.1449050026054828 NW_003726284.1 92437 84498 0.9141144779687788 1.2238722263851647 NW_003726285.1 70351 71170 1.0116416255632472 1.0535386732566725 NW_003726286.1 64646 61034 0.9441264734090277 1.0079892556132122 NW_003726287.1 69126 66610 0.9636026965251859 1.031521705379538 NW_003726288.1 227674 202425 0.8891002046786194 1.7659348111806277 NW_003726289.1 64123 63999 0.9980662164901829 1.0367354057648253 NW_003726290.1 61944 62192 1.0040036161694434 0.9771546391006277 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