BamQC report ----------------------------------- >>>>>>> Input bam file = results/0.5X_haploid_no_error_hi_variance/alignment/0.5X_haploid_no_error_hi_variance.sorted.bam outfile = results/0.5X_haploid_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 = 8,036,542 number of mapped reads = 8,036,518 (100%) number of supplementary alignments = 240 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,018,258 number of mapped paired reads (second in pair) = 4,018,260 number of mapped paired reads (both in pair) = 8,036,502 number of mapped paired reads (singletons) = 16 number of mapped bases = 1,199,124,518 bp number of sequenced bases = 1,193,368,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,640 duplication rate = 0.26% >>>>>>> Insert size mean insert size = 531.9909 std insert size = 85,368.1906 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 30.3828 >>>>>>> ACTG content number of A's = 347,232,053 bp (29.1%) number of C's = 249,462,489 bp (20.9%) number of T's = 347,244,973 bp (29.1%) number of G's = 249,427,325 bp (20.9%) number of N's = 1,985 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0511 number of mismatches = 55,648,581 number of insertions = 3,994,372 mapped reads with insertion percentage = 39.65% number of deletions = 3,993,946 mapped reads with deletion percentage = 39.51% homopolymer indels = 27.89% >>>>>>> Coverage mean coverageData = 0.4974X std coverageData = 0.7163X There is a 38.47% of reference with a coverageData >= 1X There is a 9.17% of reference with a coverageData >= 2X There is a 1.6% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 61050273 0.4976432803764726 0.71578791455904 NC_006584.3 85426708 42621214 0.4989214146002208 0.7168672449897815 NC_006585.3 91889043 45748878 0.4978708723737606 0.7163820022857015 NC_006586.3 88276631 43951720 0.49788624126355707 0.7152215932972907 NC_006587.3 88915250 44222333 0.49735374977858127 0.7158779589634592 NC_006588.3 77573801 38588482 0.4974421970118494 0.7161463479555704 NC_006589.3 80974532 40284407 0.49749478021064697 0.7140728427381933 NC_006590.3 74330416 36987365 0.4976073993720148 0.7149293320014499 NC_006591.3 61074082 30422802 0.49812950115238736 0.7157405050458308 NC_006592.3 69331447 34482342 0.4973550025574975 0.715598419481255 NC_006593.3 74389097 36995384 0.49732266544383513 0.7145184897826499 NC_006594.3 72498081 36047937 0.4972260851980344 0.7149566923799398 NC_006595.3 63241923 31460030 0.497455303501761 0.7152803721705275 NC_006596.3 60966679 30335494 0.4975749786206987 0.7148081190834193 NC_006597.3 64190966 31926742 0.4973712656076869 0.7154755843569428 NC_006598.3 59632846 29715549 0.4983084154662013 0.7165618906329798 NC_006599.3 64289059 31990662 0.4976066300799332 0.7153180751098724 NC_006600.3 55844845 27791165 0.4976496040055264 0.7158658871653933 NC_006601.3 53741614 26737224 0.49751434707562003 0.714264868127431 NC_006602.3 58134056 28911947 0.49733235540971027 0.7142741150121529 NC_006603.3 50858623 25317093 0.4977935206778996 0.7154371523507596 NC_006604.3 61439934 30551845 0.49726363638346355 0.7166136499986624 NC_006605.3 52294480 26012812 0.4974294036387779 0.714891564691166 NC_006606.3 47698779 23729963 0.4974962357002891 0.7143131503944485 NC_006607.3 51628933 25685268 0.4974975562636555 0.7159736175419679 NC_006608.3 38964690 19382134 0.4974281586739173 0.7163074210113759 NC_006609.3 45876710 22822378 0.4974719852404412 0.7177229737301706 NC_006610.3 41182112 20471707 0.4971019213390513 0.713647087171661 NC_006611.3 41845238 20807836 0.49725696386288926 0.712762885342085 NC_006612.3 40214260 20000771 0.49735519191450994 0.7161765209654362 NC_006613.3 39895921 19846994 0.4974692525584257 0.7158822602879711 NC_006614.3 38810281 19298479 0.4972517204912791 0.714534746602031 NC_006615.3 31377067 15623218 0.49791836821459445 0.7162298370173487 NC_006616.3 42124431 20954338 0.4974390752008021 0.7164969638583875 NC_006617.3 26524999 13189361 0.4972426577659814 0.7169736016253915 NC_006618.3 30810995 15324395 0.49736774161301833 0.7155346336147854 NC_006619.3 30902991 15373850 0.4974874438529267 0.7178956558697518 NC_006620.3 23914537 11905572 0.49783828137672076 0.715336658595486 NC_006621.3 123869142 61593597 0.4972473047403525 0.7159012917158583 NW_003726127.1 2660953 1325848 0.49826058558719377 0.7283462161810937 NW_003726128.1 1881673 936107 0.49748654521800545 0.7332381183612146 NW_003726129.1 1415205 709817 0.5015647909666797 0.7360534438884275 NW_003726130.1 1067467 534498 0.5007161813901507 0.7521115976278089 NW_003726131.1 866315 435828 0.5030825969768502 0.7182211665235105 NW_003726132.1 881102 439317 0.4985994811043443 0.7096707885605159 NW_003726133.1 822601 419092 0.5094717852275891 0.7249151579793262 NW_003726134.1 741967 364592 0.4913857354841927 0.7081815659446828 NW_003726135.1 745551 372233 0.4992723502483398 0.7511224969351329 NW_003726136.1 602611 297677 0.4939787026788426 0.7208365880461852 NW_003726137.1 573630 285067 0.4969527395708035 0.7063752017081717 NW_003726138.1 666183 327745 0.4919744274471129 0.7465777232678569 NW_003726139.1 557017 277516 0.49821818723665523 0.7168563318678284 NW_003726140.1 510604 256932 0.5031922977493322 0.725380076473325 NW_003726141.1 497093 247231 0.4973536139112802 0.6998074342838854 NW_003726142.1 492630 244620 0.4965592838438585 0.7384504083455885 NW_003726143.1 577062 286381 0.4962742304986293 0.7689517411392051 NW_003726144.1 561270 277962 0.4952375861884654 0.7497619570735319 NW_003726145.1 407330 205930 0.5055606019689195 0.7307561438767481 NW_003726146.1 405216 204873 0.5055896114664772 0.7403488550614817 NW_003726147.1 508668 251146 0.4937326507663152 0.7552974511766779 NW_003726148.1 540093 264642 0.4899933900272731 0.7642384440419645 NW_003726149.1 448434 219361 0.4891712046811794 0.7357913413006505 NW_003726150.1 377800 190194 0.5034250926416093 0.726918719863025 NW_003726151.1 384880 196837 0.5114243400540428 0.741453547362314 NW_003726152.1 367143 180516 0.49167762969742035 0.7253159171791173 NW_003726153.1 399987 202020 0.5050664146584763 0.7460764950532419 NW_003726154.1 376204 191667 0.5094762416135926 0.7603929822784937 NW_003726155.1 416178 207577 0.4987697571712104 0.760140766620043 NW_003726156.1 365470 182997 0.5007168851068488 0.7469503524924893 NW_003726157.1 322752 163271 0.5058713811223479 0.7228948013912216 NW_003726158.1 320591 169070 0.5273697639671732 0.7545628013632408 NW_003726159.1 310270 153935 0.49613240081219584 0.7158447937490958 NW_003726160.1 433650 216899 0.5001706445289981 0.7889629318829068 NW_003726161.1 273228 138984 0.5086740743994027 0.729258643347752 NW_003726162.1 281659 139692 0.4959614285359246 0.7184868921042267 NW_003726163.1 320442 160846 0.5019504309672265 0.7407082153460175 NW_003726164.1 265648 134973 0.5080896524724448 0.7213785175787909 NW_003726165.1 241365 124108 0.5141921985374848 0.741886078475179 NW_003726166.1 234529 117934 0.502854657632958 0.7209115663996544 NW_003726167.1 252720 130792 0.5175371953149731 0.7587213262560188 NW_003726168.1 254975 127429 0.4997705657417394 0.7678393611925497 NW_003726169.1 226053 115015 0.5087966096446409 0.7366894858275562 NW_003726170.1 223744 118895 0.531388551201373 0.7637972236866851 NW_003726171.1 227140 110296 0.48558598221361277 0.7100694171098767 NW_003726172.1 219672 110015 0.500814851232747 0.7381902258859783 NW_003726173.1 214597 109045 0.5081385107899924 0.7288122171557307 NW_003726174.1 386314 188543 0.48805634794493596 0.8456080302953853 NW_003726175.1 204342 103225 0.505158019398851 0.7186469501454378 NW_003726176.1 201724 98872 0.4901350359897682 0.7060103248886977 NW_003726177.1 216332 108307 0.5006517759739659 0.7155208335879997 NW_003726178.1 200877 101900 0.5072755965093066 0.7240354809919823 NW_003726179.1 310654 149365 0.48080823037849185 0.7866715750727706 NW_003726180.1 200932 99069 0.4930473991201003 0.702258838053709 NW_003726181.1 201410 101979 0.5063254058884862 0.7084671043673048 NW_003726182.1 292533 136987 0.4682787924781136 0.7621068670738954 NW_003726183.1 192561 96909 0.5032639007898796 0.7397506670171022 NW_003726184.1 210134 110282 0.5248174974064168 0.7559861038489981 NW_003726185.1 197844 97549 0.4930601888356483 0.7286960939373406 NW_003726186.1 196813 99112 0.5035846209345928 0.7442286315579628 NW_003726187.1 180359 93544 0.5186544613798036 0.7488150352458458 NW_003726188.1 210247 100903 0.4799259918096334 0.7609742034279673 NW_003726189.1 177735 93279 0.5248206599713056 0.7115452819697551 NW_003726190.1 172100 89537 0.5202614758861127 0.7433394426361751 NW_003726191.1 166866 86157 0.5163244759267915 0.7198028705401679 NW_003726192.1 164926 79643 0.4829014224561318 0.7031547780117225 NW_003726193.1 157598 76518 0.4855264660719045 0.7401027991874759 NW_003726194.1 143980 71692 0.4979302680927907 0.7210490385724236 NW_003726195.1 141074 70984 0.5031685498390915 0.7091509331163179 NW_003726196.1 139526 70286 0.5037484053151384 0.6977569794227276 NW_003726197.1 142260 72164 0.5072683818360748 0.7253244512645488 NW_003726198.1 138160 70842 0.5127533294730747 0.7128750181350081 NW_003726199.1 142296 70273 0.4938508461235734 0.7137359069920285 NW_003726200.1 133119 65843 0.49461759778844494 0.7168107405833488 NW_003726201.1 129748 64301 0.49558374695563706 0.687059508556171 NW_003726202.1 125962 66968 0.5316524031056985 0.7310378024510379 NW_003726203.1 127429 62484 0.49034364234201006 0.7467542337953014 NW_003726204.1 128261 66325 0.5171096436173116 0.7470390566050003 NW_003726205.1 131872 65462 0.4964056054355739 0.710489077764561 NW_003726206.1 133432 65967 0.4943866538761317 0.7417753699417565 NW_003726207.1 119670 58446 0.48839308097267486 0.6994568819709922 NW_003726208.1 144750 69488 0.4800552677029361 0.759146499912979 NW_003726209.1 120779 60311 0.4993500525753649 0.7260604077049518 NW_003726210.1 115952 57637 0.4970763764316269 0.7055276895322378 NW_003726211.1 118237 58413 0.49403317066569685 0.7047421086466152 NW_003726212.1 111908 57763 0.5161650641598455 0.7364231441045356 NW_003726213.1 117332 60156 0.5126990079432721 0.7583835621022842 NW_003726214.1 111759 55514 0.4967295698780411 0.7310562027440085 NW_003726215.1 108801 53180 0.4887822722217627 0.7321285084021086 NW_003726216.1 112014 58768 0.5246487046262074 0.7439350266015996 NW_003726217.1 106428 52120 0.48972075017852446 0.683284647383354 NW_003726218.1 104912 52179 0.49735969193228613 0.6952121035812986 NW_003726219.1 104646 51350 0.49070198574240775 0.7112784544390649 NW_003726220.1 103248 51823 0.5019273981094065 0.7107162692487503 NW_003726221.1 129482 66580 0.5142027463276749 0.7993011177149694 NW_003726222.1 118473 59293 0.5004769019101398 0.7544627968636706 NW_003726223.1 99993 49248 0.49251447601332093 0.7196170759407945 NW_003726224.1 109585 54573 0.4979969886389561 0.7268476902817679 NW_003726225.1 124049 60514 0.48782336012382205 0.7734892075138342 NW_003726226.1 99658 48232 0.4839751951674728 0.6762540898436529 NW_003726227.1 101741 50407 0.4954443144848193 0.7354302482170543 NW_003726228.1 97365 50184 0.5154213526421199 0.7491466592870242 NW_003726229.1 94395 45440 0.48138142910111764 0.7081885576390026 NW_003726230.1 102992 48285 0.46882282118999535 0.7268070360077787 NW_003726231.1 95509 45646 0.4779235464720602 0.726924639948355 NW_003726232.1 92047 43584 0.4734972351081513 0.7390196578496935 NW_003726233.1 87753 47703 0.5436053468257496 0.776141833106082 NW_003726234.1 96536 46240 0.4789922930305793 0.7094766722780094 NW_003726235.1 86544 42793 0.4944652431133296 0.67064929108895 NW_003726236.1 85476 42921 0.5021409518461323 0.6636601968466589 NW_003726237.1 110512 58535 0.5296709859562763 0.7994589068208792 NW_003726238.1 83291 41734 0.5010625397702032 0.7546595579563612 NW_003726239.1 82459 44365 0.5380249578578445 0.7440449994217244 NW_003726240.1 81605 42567 0.5216224496048036 0.7621296029028297 NW_003726241.1 82380 40894 0.4964068948773974 0.7358994902115679 NW_003726242.1 102198 48425 0.4738351044051743 0.7494526172192895 NW_003726243.1 82108 40305 0.490877868173625 0.7771405820967937 NW_003726244.1 87041 40632 0.46681448972323386 0.7304555446496158 NW_003726245.1 79722 39132 0.4908557236396478 0.684183006049114 NW_003726246.1 230124 113504 0.4932297370113504 0.9786116846157656 NW_003726247.1 78357 39641 0.5059024720190921 0.7125060255067089 NW_003726248.1 256406 125234 0.4884207077837492 1.0195937898168224 NW_003726249.1 78050 37596 0.4816912235746316 0.6579918386492005 NW_003726250.1 81930 39615 0.4835225192237276 0.6789238771285544 NW_003726251.1 77100 39474 0.5119844357976654 0.7717298843431604 NW_003726252.1 77130 37829 0.4904576688707377 0.6819538219985763 NW_003726253.1 79078 38583 0.4879106704772503 0.725980742307756 NW_003726254.1 90550 45918 0.5071010491441192 0.7800364887262827 NW_003726255.1 82767 42040 0.507931905227929 0.7076696834337254 NW_003726256.1 89070 42899 0.48163242393622996 0.7162608942720775 NW_003726257.1 97802 47426 0.48491850882395043 0.7483913917013516 NW_003726258.1 79712 39686 0.4978673223604978 0.6850008405066665 NW_003726259.1 79581 36771 0.4620575262939646 0.7147651263928045 NW_003726260.1 73720 35787 0.48544492674986434 0.6891265411578843 NW_003726261.1 97799 45285 0.46304154439206946 0.7362452632151341 NW_003726262.1 73171 33704 0.4606196443946372 0.6954706172784032 NW_003726263.1 104732 49596 0.47355154107627084 0.8062412165249165 NW_003726264.1 78935 36663 0.4644707670868436 0.7559590538389866 NW_003726265.1 72992 37308 0.5111245067952652 0.7344847599689766 NW_003726266.1 68721 34317 0.4993670057187759 0.7338432445715584 NW_003726267.1 73611 34360 0.46677806306122727 0.6866350369930937 NW_003726268.1 68272 34038 0.4985645652683384 0.7006500698906134 NW_003726269.1 79297 39976 0.5041300427506715 0.7390059160544635 NW_003726270.1 84443 36811 0.43592719349146763 0.6835078010252519 NW_003726271.1 80679 38360 0.47546449509785693 0.7243366280221165 NW_003726272.1 68834 34562 0.5021065171281635 0.7390324153792978 NW_003726273.1 67496 33124 0.49075500770416025 0.7017481924669605 NW_003726274.1 66523 33182 0.49880492461254 0.732714674417135 NW_003726275.1 67057 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