BamQC report ----------------------------------- >>>>>>> Input bam file = SRR7062655_1.bam outfile = SRR7062655_1/genome_results.txt >>>>>>> Reference number of bases = 1,230,258,557 bp number of contigs = 23475 >>>>>>> Globals number of windows = 23874 number of reads = 374,682,930 number of mapped reads = 373,764,495 (99.75%) number of secondary alignments = 448,939 number of mapped paired reads (first in pair) = 186,895,312 number of mapped paired reads (second in pair) = 186,869,183 number of mapped paired reads (both in pair) = 373,438,366 number of mapped paired reads (singletons) = 326,129 number of mapped bases = 33,461,241,714 bp number of sequenced bases = 33,437,856,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,253,411 duplication rate = 21.69% >>>>>>> Insert size mean insert size = 28,089.555 std insert size = 1,509,384.9159 median insert size = 477 >>>>>>> Mapping quality mean mapping quality = 7.6676 >>>>>>> ACTG content number of A's = 9,868,576,455 bp (29.51%) number of C's = 6,868,381,166 bp (20.54%) number of T's = 9,872,419,615 bp (29.52%) number of G's = 6,823,552,283 bp (20.41%) number of N's = 4,926,622 bp (0.01%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 278,723,511 number of insertions = 8,314,089 mapped reads with insertion percentage = 2.15% number of deletions = 9,100,974 mapped reads with deletion percentage = 2.35% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 27.1985X std coverageData = 31.1725X There is a 90.9% of reference with a coverageData >= 1X There is a 89.82% of reference with a coverageData >= 2X There is a 89.09% of reference with a coverageData >= 3X There is a 88.48% of reference with a coverageData >= 4X There is a 87.93% of reference with a coverageData >= 5X There is a 87.4% of reference with a coverageData >= 6X There is a 86.87% of reference with a coverageData >= 7X There is a 86.34% of reference with a coverageData >= 8X There is a 85.78% of reference with a coverageData >= 9X There is a 85.2% of reference with a coverageData >= 10X There is a 84.58% of reference with a coverageData >= 11X There is a 83.92% of reference with a coverageData >= 12X There is a 83.2% of reference with a coverageData >= 13X There is a 82.41% of reference with a coverageData >= 14X There is a 81.55% of reference with a coverageData >= 15X There is a 80.61% of reference with a coverageData >= 16X There is a 79.57% of reference with a coverageData >= 17X There is a 78.41% of reference with a coverageData >= 18X There is a 77.12% of reference with a coverageData >= 19X There is a 75.65% of reference with a coverageData >= 20X There is a 73.98% of reference with a coverageData >= 21X There is a 72.08% of reference with a coverageData >= 22X There is a 69.91% of reference with a coverageData >= 23X There is a 67.45% of reference with a coverageData >= 24X There is a 64.68% of reference with a coverageData >= 25X There is a 61.61% of reference with a coverageData >= 26X There is a 58.24% of reference with a coverageData >= 27X There is a 54.61% of reference with a coverageData >= 28X There is a 50.76% of reference with a coverageData >= 29X There is a 46.74% of reference with a coverageData >= 30X There is a 42.63% of reference with a coverageData >= 31X There is a 38.5% of reference with a coverageData >= 32X There is a 34.41% of reference with a coverageData >= 33X There is a 30.45% of reference with a coverageData >= 34X There is a 26.66% of reference with a coverageData >= 35X There is a 23.12% of reference with a coverageData >= 36X There is a 19.84% of reference with a coverageData >= 37X There is a 16.88% of reference with a coverageData >= 38X There is a 14.23% of reference with a coverageData >= 39X There is a 11.9% of reference with a coverageData >= 40X There is a 9.89% of reference with a coverageData >= 41X There is a 8.17% of reference with a coverageData >= 42X There is a 6.73% of reference with a coverageData >= 43X There is a 5.53% of reference with a coverageData >= 44X There is a 4.55% of reference with a coverageData >= 45X There is a 3.76% of reference with a coverageData >= 46X There is a 3.13% of reference with a coverageData >= 47X There is a 2.63% of reference with a coverageData >= 48X There is a 2.23% of reference with a coverageData >= 49X There is a 1.93% of reference with a coverageData >= 50X There is a 1.69% of reference with a coverageData >= 51X >>>>>>> Coverage per contig 1 196202544 6010279034 30.633033147623202 9.564337367964377 2 149560735 4595097555 30.723956759105256 9.688537891278049 3 111302122 3427069455 30.790692876457467 12.899607998413686 4 91282656 2803786744 30.715437815481618 10.31361360874357 5 59825302 1809116171 30.239983928539132 9.28289873830049 6 35467016 1056198126 29.779729030488497 9.702371279499221 7 36946936 1103082030 29.855845962436508 9.677440300961397 8 29963013 879575911 29.355389292792417 10.716729059535226 9 24091566 699476827 29.034095458966842 9.830345180958316 10 20435342 585728290 28.662514676779082 10.04277595046139 11 20218793 588592915 29.111179633719974 11.932188178278976 12 19948154 587249374 29.438782856799683 9.281170795265217 13 18407460 511034331 27.76234912367051 10.221549763579908 14 15595052 430091230 27.578698038326515 10.80637562673419 15 12762846 362149788 28.375315975762774 11.109007174215641 16 652338 9608165 14.72881389709016 25.231861023944315 17 10956400 286032502 26.106431127012524 13.434693832196508 18 11053727 305172968 27.6081513502188 9.406988473994074 19 9979828 274614592 27.51696642467185 9.255536000025758 20 14109371 397426953 28.167588264565445 14.360420563813252 21 6862722 187450431 27.31429759212161 17.08103313134392 22 4729743 113694337 24.038163807208974 14.477552728521058 23 5786528 145260634 25.10324567685493 10.563737933432362 24 6280547 165125902 26.291643387112618 8.332381155535693 25 2906300 45231364 15.56321233183085 15.21748913077514 26 5313770 128600144 24.20130039501145 11.062200794892581 27 5655794 126787360 22.417252113496353 13.468306995807346 28 4974273 117399024 23.6012426338482 44.59633611251582 30 24927 180927 7.258274160548803 8.431314771401887 31 49161 564089 11.474319074062773 12.94241228698767 32 78254 859079 10.978084187389783 9.577491350972945 33 1648031 28927614 17.55283365422131 12.582968078608848 W 5160035 4396004 0.8519329810747408 3.891234949077169 Z 82310166 2602548818 31.618801716424677 13.29606532538446 MT 16775 200746 11.966974664679583 4.057398304135129 LGE64 897576 25562610 28.47960506965427 25.179616469130213 KQ759483.1 1265006 38295667 30.273110957576485 33.558762624748304 KQ759505.1 498515 5291515 10.61455522903022 8.30095934129019 KQ759404.1 476228 14287413 30.00120320518743 32.00878825238842 AADN04000541.1 371203 11694144 31.503366082709462 33.36667676916064 KQ759506.1 234913 3542464 15.079897664241656 5.236132660149309 KQ759543.1 226491 32607 0.1439659854033935 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KQ759528.1 113001 1734226 15.346996929230714 14.914545038389713 KQ759510.1 111981 1623345 14.496611032228682 6.304993618292838 AADN04000659.1 99212 2181997 21.993277022940774 13.266345791083765 AADN04000661.1 96849 2094400 21.625416886080394 15.276517163679895 AADN04000662.1 96062 2161418 22.500239428702297 21.209055450726854 AADN04000668.1 90963 2276854 25.03055088332619 11.583458990964807 KQ759529.1 90829 15717 0.1730394477534708 0.8683473555642695 KQ759530.1 87745 3536299 40.302000113966606 206.03975972710805 AADN04000677.1 87083 2778717 31.908834100800387 96.19278433405324 AADN04000682.1 85355 2756953 32.29984183703357 31.23931315872575 KQ759486.1 84856 23577 0.27784717639294804 1.489963328412352 KQ759511.1 84478 880697 10.425163948010132 6.904870942503895 KQ759531.1 84196 75318 0.8945555608342439 3.469138404027621 KQ759532.1 83724 2272865 27.147114328030195 15.084850344614082 KQ759480.1 81621 1449545 17.75946141311672 10.561175311267492 KQ759534.1 81551 676526 8.295741315250579 10.186546321567885 KQ759533.1 81163 1658665 20.436220938112193 23.078482964099415 AADN04000704.1 80105 2115200 26.40534298732913 11.22870421109272 AADN04000706.1 79378 1204170 15.17007231222757 13.25589094312179 AADN04000708.1 78622 864872 11.000381572587825 16.670641668037273 AADN04000710.1 77859 1299051 16.684660732863254 17.10694695145252 AADN04000712.1 77675 147879 1.9038171869971032 5.194246955549796 AADN04000711.1 77392 23632 0.3053545586107091 1.5187711147631937 AADN04000717.1 76721 1034518 13.484156880124086 8.953178301236957 KQ759535.1 76388 1016359 13.305218097083312 6.765896813832093 KQ759536.1 76109 612066 8.041966127527624 7.937608622216477 AADN04000729.1 74004 5231070 70.68631425328361 80.56312626479944 AADN04000732.1 73820 457634 6.19932267678136 7.713449969351665 AADN04000736.1 70062 2650174 37.82612543176044 23.38100584735186 AADN04000737.1 69917 1053688 15.070555086745713 11.303965505150984 KQ759537.1 68154 5923773 86.91746632626112 385.6493688134336 AADN04000744.1 67341 1334141 19.811719457685513 10.745297693834896 AADN04000745.1 64791 959271 14.805621151085798 11.081816355356542 KQ759334.1 64707 480355 7.4235399570371055 9.892875692243717 KQ759538.1 64595 821103 12.711556622029569 19.32891503413963 AADN04000750.1 64410 2119525 32.90676913522745 30.105207700186238 AADN04000751.1 64267 2023289 31.482549364370517 26.570756633527896 AADN04000752.1 64035 137066 2.1404856718981806 5.501737236353013 AADN04000753.1 63752 890622 13.97010289873259 6.908702424126308 KQ759539.1 63582 735746 11.571608316819226 12.955469404297878 AADN04000754.1 63536 26987 0.4247513220851171 1.7561194419076789 KQ759487.1 63071 15328 0.24302769894246168 1.0244769414368593 KQ759540.1 63037 11466 0.1818931738502784 1.313561910268631 AADN04000767.1 61976 2876190 46.40812572608752 71.58691897659507 KQ759541.1 60946 355651 5.835510123716077 12.789638629597617 KQ759466.1 60160 2633180 43.769614361702125 43.94929408255501 AADN04000772.1 60150 65379 1.0869326683291771 6.999021201277071 KQ759365.1 59978 51022 0.8506785821467872 2.7631589226890356 AADN04000776.1 59694 968912 16.231313029785237 7.795935971595643 AADN04000777.1 59540 898552 15.091568693315418 16.157013512201363 KQ759542.1 59175 9835 0.16620194338825517 1.1072629048262153 AADN04000780.1 59125 2053107 34.724854122621565 74.49134950523016 AADN04000785.1 57913 1953720 33.73543073230535 49.385088646715076 AADN04000787.1 57900 1846961 31.89915371329879 26.550412937012087 AADN04000789.1 57687 1022379 17.722866503718343 29.84033533377573 AADN04000788.1 57649 81853 1.4198511682769865 11.058694998764974 AADN04000790.1 56914 503730 8.850722142179428 10.86794812041637 AADN04000792.1 56491 1630878 28.869696057779116 11.049550785611268 KQ759392.1 55852 1554940 27.84036381866361 13.056247577745813 AADN04000799.1 55430 1391168 25.097744903481868 11.74864390534096 AADN04000798.1 55229 43784 0.792771913306415 2.407113151588551 KQ759335.1 54779 5242 0.09569360521367677 0.6563731525835955 AADN04000801.1 53922 1634355 30.30961388672527 91.8519441998283 AADN04000802.1 53480 11267 0.2106768885564697 0.969209050492777 AADN04000803.1 53392 632854 11.852974228348817 9.874407190941096 KQ759544.1 53158 732459 13.778904398209113 13.138890962551312 KQ759454.1 53068 274656 5.175548353056456 7.041112564105136 KQ759545.1 52844 6300 0.1192188327908561 0.7004868493229695 KQ759481.1 52784 623417 11.810719157320401 12.010687523013186 AADN04000814.1 52690 2656687 50.42108559498956 54.96033838585358 AADN04000815.1 52096 250796 4.814112407862408 8.814312385183024 KQ759488.1 51788 26722 0.5159882598285317 2.2581819038131576 KQ759546.1 51687 718376 13.898581848433842 12.534432954981016 AADN04000827.1 51294 291561 5.684115101181424 8.161252375690365 AADN04000828.1 51194 30621 0.5981365003711372 1.7183689658919645 AADN04000829.1 50833 2812409 55.326441484862194 78.65352955454603 KQ759489.1 50595 10367 0.20490167012550647 1.1719229177787247 AADN04000831.1 50160 160966 3.2090510366826157 6.08503727519164 AADN04000832.1 50079 875149 17.475368917110966 16.321605343448876 AADN04000833.1 50010 660033 13.198020395920816 20.317225866491942 AADN04000834.1 49882 2553203 51.18485626077543 47.387165798999206 AADN04000835.1 49741 49217 0.9894654309322289 1.7369483486947082 AADN04000839.1 49566 598170 12.068151555501755 12.631251537264092 KQ759547.1 49554 1244636 25.116761512693223 29.547320075179645 AADN04000838.1 49481 221465 4.4757583719003255 5.754945733709132 KQ759548.1 49166 62639 1.2740308343163975 4.650666282687678 AADN04000843.1 48646 43895 0.9023352382518603 4.273367763829248 KQ759549.1 47964 709129 14.78460929030106 9.392264625639806 AADN04000848.1 47841 1114037 23.286239836123826 11.901434484122877 AADN04000849.1 47738 274583 5.751874816707864 7.352203951711377 AADN04000850.1 47215 722249 15.297024250767764 10.100650788354422 KQ759455.1 46957 173541 3.6957429137295823 5.7652295620650085 KQ759513.1 46489 4163 0.08954806513368754 0.7267432856276792 AADN04000858.1 46233 789076 17.06737611662665 17.711107201037578 AADN04000861.1 45885 814144 17.743140459845264 18.83528746991871 AADN04000863.1 45565 303535 6.661582354877647 17.1245670456917 AADN04000864.1 45392 1501531 33.079198977793446 31.400611010930035 AADN04000865.1 45384 1104453 24.335735060814383 13.45371456292036 AADN04000866.1 45367 895604 19.74130976260277 25.130069603921168 AADN04000867.1 45304 451600 9.968214727176408 21.50069874559795 AADN04000868.1 45289 215257 4.752964295965908 9.135385528331506 AADN04000869.1 45021 1268964 28.186046511627907 25.89913596859483 AADN04000857.1 44988 103388 2.298123944162888 4.886686534800447 KQ759514.1 44970 597510 13.28685790527018 7.3011639379815865 AADN04000872.1 44775 476813 10.649089893914015 21.665582722327454 AADN04000873.1 44769 2757477 61.59344635797092 113.20664643595875 AADN04000874.1 44695 907437 20.302875041951 19.46415095309632 AADN04000875.1 44461 214263 4.819122376914599 24.15079301264268 AADN04000876.1 44362 16163 0.3643433569270998 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