BamQC report ----------------------------------- >>>>>>> Input bam file = SRR7062654.recal.bam outfile = SRR7062654.recal/genome_results.txt >>>>>>> Reference number of bases = 1,230,258,557 bp number of contigs = 23475 >>>>>>> Globals number of windows = 23874 number of reads = 371,207,878 number of mapped reads = 370,874,029 (99.91%) number of secondary alignments = 425,104 number of mapped paired reads (first in pair) = 185,448,134 number of mapped paired reads (second in pair) = 185,425,895 number of mapped paired reads (both in pair) = 370,540,180 number of mapped paired reads (singletons) = 333,849 number of mapped bases = 32,117,502,881 bp number of sequenced bases = 32,095,072,891 bp number of aligned bases = 0 bp number of duplicated reads (flagged) = 12,226,624 >>>>>>> Insert size mean insert size = 28,941.2277 std insert size = 1,533,913.0146 median insert size = 479 >>>>>>> Mapping quality mean mapping quality = 7.6077 >>>>>>> ACTG content number of A's = 9,475,051,647 bp (29.52%) number of C's = 6,576,731,582 bp (20.49%) number of T's = 9,466,472,518 bp (29.5%) number of G's = 6,570,540,597 bp (20.47%) number of N's = 6,276,547 bp (0.02%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 265,025,577 number of insertions = 7,865,638 mapped reads with insertion percentage = 2.05% number of deletions = 8,637,774 mapped reads with deletion percentage = 2.25% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 26.1063X std coverageData = 23.6357X There is a 90.77% of reference with a coverageData >= 1X There is a 89.69% of reference with a coverageData >= 2X There is a 88.96% of reference with a coverageData >= 3X There is a 88.35% of reference with a coverageData >= 4X There is a 87.79% of reference with a coverageData >= 5X There is a 87.26% of reference with a coverageData >= 6X There is a 86.73% of reference with a coverageData >= 7X There is a 86.18% of reference with a coverageData >= 8X There is a 85.62% of reference with a coverageData >= 9X There is a 85.03% of reference with a coverageData >= 10X There is a 84.39% of reference with a coverageData >= 11X There is a 83.71% of reference with a coverageData >= 12X There is a 82.97% of reference with a coverageData >= 13X There is a 82.16% of reference with a coverageData >= 14X There is a 81.28% of reference with a coverageData >= 15X There is a 80.31% of reference with a coverageData >= 16X There is a 79.23% of reference with a coverageData >= 17X There is a 78.03% of reference with a coverageData >= 18X There is a 76.67% of reference with a coverageData >= 19X There is a 75.11% of reference with a coverageData >= 20X There is a 73.31% of reference with a coverageData >= 21X There is a 71.24% of reference with a coverageData >= 22X There is a 68.86% of reference with a coverageData >= 23X There is a 66.14% of reference with a coverageData >= 24X There is a 63.06% of reference with a coverageData >= 25X There is a 59.64% of reference with a coverageData >= 26X There is a 55.9% of reference with a coverageData >= 27X There is a 51.88% of reference with a coverageData >= 28X There is a 47.65% of reference with a coverageData >= 29X There is a 43.28% of reference with a coverageData >= 30X There is a 38.87% of reference with a coverageData >= 31X There is a 34.5% of reference with a coverageData >= 32X There is a 30.25% of reference with a coverageData >= 33X There is a 26.21% of reference with a coverageData >= 34X There is a 22.44% of reference with a coverageData >= 35X There is a 18.99% of reference with a coverageData >= 36X There is a 15.89% of reference with a coverageData >= 37X There is a 13.17% of reference with a coverageData >= 38X There is a 10.81% of reference with a coverageData >= 39X There is a 8.8% of reference with a coverageData >= 40X There is a 7.13% of reference with a coverageData >= 41X There is a 5.75% of reference with a coverageData >= 42X There is a 4.63% of reference with a coverageData >= 43X There is a 3.75% of reference with a coverageData >= 44X There is a 3.05% of reference with a coverageData >= 45X There is a 2.51% of reference with a coverageData >= 46X There is a 2.09% of reference with a coverageData >= 47X There is a 1.77% of reference with a coverageData >= 48X There is a 1.54% of reference with a coverageData >= 49X There is a 1.36% of reference with a coverageData >= 50X There is a 1.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig 1 196202544 5812806675 29.62656118770815 9.061941573541947 2 149560735 4438946909 29.679894987143516 9.523450615206848 3 111302122 3315030011 29.784068366639048 12.76282402711394 4 91282656 2709626657 29.683915606048974 9.160543026191705 5 59825302 1759013756 29.402505247696034 8.780790546437922 6 35467016 1030071318 29.043078165921823 9.262881098803941 7 36946936 1070885218 28.984412076822824 8.98654012978208 8 29963013 858175546 28.64116322347155 10.531576732724993 9 24091566 684880687 28.4282344701046 9.424885755579531 10 20435342 574656108 28.120699325707395 9.956388832552133 11 20218793 573780881 28.37859218401415 11.667934507047322 12 19948154 573862320 28.767690484041783 8.814982061573074 13 18407460 500965770 27.215366487282875 9.840822808262985 14 15595052 424858601 27.24316667876452 11.093569600663535 15 12762846 356296971 27.916733540465817 9.057938330913565 16 652338 9747899 14.943018803135798 18.479684881391705 17 10956400 280664154 25.616457413018875 10.258290110416647 18 11053727 302062426 27.326749249370824 9.384550501083135 19 9979828 272869100 27.342064412332558 9.261681760956643 20 14109371 392289792 27.80349258659369 11.557971323373051 21 6862722 183147530 26.68730133611707 10.336926479323122 22 4729743 111976236 23.674909186397652 12.641297413222672 23 5786528 145719808 25.182597924005552 9.70699635214062 24 6280547 164247926 26.15185046780161 7.951225313929248 25 2906300 45635463 15.702254756907408 13.76878138568424 26 5313770 128879612 24.25389356332698 9.66251275357075 27 5655794 127926618 22.618684131706353 13.43494458421315 28 4974273 116825509 23.48594638854763 23.33272449833538 30 24927 176154 7.066795041521242 8.582555769875322 31 49161 583718 11.873598991070157 15.172501345063415 32 78254 942284 12.041352518721087 10.316624022813617 33 1648031 29110652 17.66389831259242 12.413618889250023 W 5160035 4158513 0.8059079056634306 4.052834425345936 Z 82310166 2493819403 30.29782983307311 12.414788510141568 MT 16775 432708 25.794813710879286 6.685850500031139 LGE64 897576 21813195 24.30233762934838 18.758235454817463 KQ759483.1 1265006 42007364 33.20724486682277 33.40918962830137 KQ759505.1 498515 5383653 10.799380159072445 8.492599906502864 KQ759404.1 476228 17717737 37.20431599989921 34.21843706098343 AADN04000541.1 371203 13892318 37.42512318057774 36.49174763602657 KQ759506.1 234913 3510250 14.942766045301878 5.108457674422493 KQ759543.1 226491 32296 0.14259286240954386 1.2243910554693564 KQ759405.1 212434 4792817 22.561440259092237 14.255441345878259 AADN04000593.1 209746 6883984 32.82057345551286 33.61654277546588 KQ759507.1 174450 2541772 14.570203496703927 5.398459127412468 AADN04000612.1 150454 3119082 20.731133768460793 10.704783885845668 KQ759527.1 143297 3908106 27.272769143806222 31.860348033507677 AADN04000623.1 140921 1686669 11.968897467375339 10.196259226036249 KQ759508.1 140174 2107639 15.03587683878608 5.548547857445875 AADN04000624.1 140122 3878886 27.682205506629938 23.14396308249609 AADN04000628.1 137062 3761583 27.444390130014153 25.998776840343623 AADN04000631.1 135147 3847977 28.47252991187374 10.250982509607644 KQ759484.1 129908 1617270 12.449348769898698 11.185090386220061 AADN04000639.1 125782 3532629 28.085330174428773 9.04317230358972 AADN04000640.1 125648 1585037 12.614900356551637 14.205274352554621 KQ759509.1 122550 1829385 14.92766217870257 5.22925263292924 AADN04000646.1 115712 52713 0.45555344303097345 1.8926244514918926 KQ759528.1 113001 2721286 24.081963876425874 21.329816807198537 KQ759510.1 111981 1619207 14.459658334896098 6.42191653394716 AADN04000659.1 99212 2232756 22.50489860097569 13.460846368089998 AADN04000661.1 96849 2155604 22.257369719873203 14.03432957801486 AADN04000662.1 96062 2053850 21.38046261789261 17.541266678781714 AADN04000668.1 90963 2214194 24.34169937227224 11.198624246021435 KQ759529.1 90829 13222 0.14557024738794877 0.851062931269694 KQ759530.1 87745 2351096 26.794643569434157 38.98800934541792 AADN04000677.1 87083 2248216 25.816933270557975 76.65300747873114 AADN04000682.1 85355 3276457 38.38623396403257 31.861777127088022 KQ759486.1 84856 21199 0.24982322994249082 1.8362606986491556 KQ759511.1 84478 883184 10.454603565425318 6.611561202044706 KQ759531.1 84196 63254 0.7512708442206281 2.735787715883578 KQ759532.1 83724 2077540 24.814151258898285 13.4584487355895 KQ759480.1 81621 1461378 17.904436358290145 10.1389214332738 KQ759534.1 81551 691911 8.484396267366433 9.934633153833952 KQ759533.1 81163 2168722 26.720574646082575 25.923046915547346 AADN04000704.1 80105 2090469 26.096610698458274 10.96807325185936 AADN04000706.1 79378 1218934 15.35606843205926 12.77820745830324 AADN04000708.1 78622 782412 9.95156571951871 13.94375205025949 AADN04000710.1 77859 1253343 16.097599506800755 15.46298314856129 AADN04000712.1 77675 133293 1.7160347602188606 4.8992650749185085 AADN04000711.1 77392 23851 0.3081843084556543 1.6032800028171124 AADN04000717.1 76721 1051254 13.702297936679658 8.269431366543927 KQ759535.1 76388 999788 13.088286118238466 6.578756037985262 KQ759536.1 76109 619758 8.143031704529031 8.451502905686997 AADN04000729.1 74004 3806764 51.43997621750176 62.43701519300899 AADN04000732.1 73820 450878 6.107802763478732 7.783078123453035 AADN04000736.1 70062 1346335 19.216336958693727 16.092201095989058 AADN04000737.1 69917 1100901 15.745827195102764 11.19315364052955 KQ759537.1 68154 2109859 30.95722921618687 64.47021937895803 AADN04000744.1 67341 1356591 20.145097340401836 10.682233474958604 AADN04000745.1 64791 955267 14.743822444475313 10.603030065286287 KQ759334.1 64707 819972 12.67207566414762 15.66230388950442 KQ759538.1 64595 587396 9.093521170369224 12.960686489050818 AADN04000750.1 64410 2567773 39.86606117062568 36.57237931451161 AADN04000751.1 64267 1913889 29.780276035912678 23.781189900030448 AADN04000752.1 64035 155012 2.4207386585461075 5.776716887356595 AADN04000753.1 63752 848410 13.30797465177563 6.488695177799602 KQ759539.1 63582 753522 11.851184297442673 14.051399610155933 AADN04000754.1 63536 30579 0.48128619994963484 2.130310043408228 KQ759487.1 63071 16552 0.26243439932774176 1.3812769693844547 KQ759540.1 63037 6938 0.11006234433745261 0.8547513841361036 AADN04000767.1 61976 1754760 28.313540725442106 49.779508781198075 KQ759541.1 60946 340414 5.585501919732222 10.291204935479197 KQ759466.1 60160 2237807 37.197589760638294 39.65680096385921 AADN04000772.1 60150 74340 1.2359102244389026 8.733339950806414 KQ759365.1 59978 67624 1.127480076027877 3.9611216992480003 AADN04000776.1 59694 1024076 17.155426005963747 8.077518905004567 AADN04000777.1 59540 870522 14.62079274437353 14.81673859891002 KQ759542.1 59175 11464 0.19373046049852133 1.3961739190657407 AADN04000780.1 59125 1937886 32.7760845665962 84.20009936537976 AADN04000785.1 57913 1704584 29.433529604751957 39.53958827365641 AADN04000787.1 57900 1220343 21.076735751295338 18.188744441830757 AADN04000789.1 57687 1026699 17.797753393312185 32.90740511663883 AADN04000788.1 57649 73797 1.2801089351072872 9.955537904466091 AADN04000790.1 56914 522931 9.188090803668693 10.66433236293238 AADN04000792.1 56491 1539220 27.24717211591227 10.273378984744037 KQ759392.1 55852 1467861 26.28126119028862 13.303566807083829 AADN04000799.1 55430 1352613 24.40218293342955 11.098567941869135 AADN04000798.1 55229 46784 0.8470912020858606 3.119017863855548 KQ759335.1 54779 5241 0.09567535004289965 0.7784859732191853 AADN04000801.1 53922 1085409 20.129242238789363 38.57339192140255 AADN04000802.1 53480 11884 0.22221391174270755 0.9444514100258297 AADN04000803.1 53392 561593 10.518298621516331 7.898446722567151 KQ759544.1 53158 610507 11.484762406411077 11.68565719052014 KQ759454.1 53068 295954 5.576882490389688 7.452343989793888 KQ759545.1 52844 7195 0.1361554764968587 0.6929328655407316 KQ759481.1 52784 631537 11.964553652622007 12.144231207309724 AADN04000814.1 52690 2912597 55.277984437274625 60.71556487621969 AADN04000815.1 52096 203884 3.9136210073710074 7.240861267349493 KQ759488.1 51788 22269 0.43000308951880745 1.9637851464799503 KQ759546.1 51687 743789 14.390252868226053 14.950715902022655 AADN04000827.1 51294 395262 7.705813545443911 10.474958378661713 AADN04000828.1 51194 48346 0.9443684806813298 2.896647459902322 AADN04000829.1 50833 2068803 40.69803080675939 51.296492530666576 KQ759489.1 50595 9156 0.18096649866587608 0.770376992317186 AADN04000831.1 50160 162326 3.236164274322169 6.936562944201052 AADN04000832.1 50079 753384 15.043910621218474 12.50467772536583 AADN04000833.1 50010 521654 10.430993801239753 15.713254383431146 AADN04000834.1 49882 1678949 33.65841385670181 32.79620048795428 AADN04000835.1 49741 45958 0.9239460404897368 1.759175033787264 AADN04000839.1 49566 738125 14.891760480974861 16.783467337060365 KQ759547.1 49554 1233677 24.895608830770474 27.131305351187326 AADN04000838.1 49481 384216 7.76491986823225 7.0704255339791455 KQ759548.1 49166 52694 1.0717569051783753 4.249135712591356 AADN04000843.1 48646 31798 0.6536611437733832 3.1997953952153093 KQ759549.1 47964 713934 14.884788591443582 10.016930393614233 AADN04000848.1 47841 1015910 21.235133044877823 12.935287426385582 AADN04000849.1 47738 268842 5.631614227659307 7.736809900632719 AADN04000850.1 47215 676480 14.327650111193476 9.383983596908418 KQ759455.1 46957 212604 4.5276316630108395 6.406678264018952 KQ759513.1 46489 3357 0.07221063047172449 0.44227192263323895 AADN04000858.1 46233 550986 11.917591330867563 13.346917632086413 AADN04000861.1 45885 626961 13.663746322327558 12.005028648740872 AADN04000863.1 45565 206821 4.539032151870954 10.51349059436898 AADN04000864.1 45392 1235928 27.227881565033485 23.910010576070526 AADN04000865.1 45384 1059662 23.34880133967918 12.688722144294688 AADN04000866.1 45367 1760623 38.80845107677386 42.065839084356 AADN04000867.1 45304 361132 7.9713049620342575 15.291056924817575 AADN04000868.1 45289 179301 3.9590408266908077 8.615163606073247 AADN04000869.1 45021 1173350 26.062282046156238 22.992352186002986 AADN04000857.1 44988 99651 2.2150573486263005 4.771188187371358 KQ759514.1 44970 547973 12.185301311985768 6.649742734078259 AADN04000872.1 44775 550708 12.299452819653824 23.568590542406383 AADN04000873.1 44769 1918351 42.84998548102482 59.30407500236836 AADN04000874.1 44695 719016 16.08716858709028 15.9409041183651 AADN04000875.1 44461 163057 3.6674163873956953 11.223932147770697 AADN04000876.1 44362 17001 0.3832333979532032 1.3642516484153089 AADN04000877.1 44203 124030 2.8059181503517863 10.697528318400288 AADN04000879.1 43509 1234 0.0283619481026914 0.30682694942800764 KQ759550.1 43298 244740 5.652455078756525 6.686303056968461 AADN04000878.1 43025 567688 13.194375363160953 5.538875238627164 AADN04000886.1 42768 2538955 59.36576412270857 53.97344746888948 KQ759490.1 42671 46422 1.0879051346347637 3.615971727962579 AADN04000890.1 42655 799204 18.73646700269605 17.45560276770957 AADN04000891.1 42544 311554 7.32310078977059 8.097474033571745 AADN04000892.1 42175 390292 9.254107883817428 10.648773633292471 AADN04000894.1 42076 173966 4.134566023386253 7.0167129139623015 AADN04000895.1 42011 728562 17.342172288210232 16.54353755877508 AADN04000896.1 41836 461401 11.028802944832202 12.42551341105748 AADN04000898.1 41756 224165 5.368450043107577 8.89182291597941 AADN04000897.1 41744 254341 6.0928756228440015 7.001433728627436 KQ759551.1 41656 585864 14.064336470136356 5.4967428802330325 AADN04000901.1 41546 291201 7.009122418524045 20.317855388246432 AADN04000902.1 41531 265179 6.3850858394933905 8.071239709490259 AADN04000903.1 41278 1471606 35.65109743689132 56.88065077380222 AADN04000905.1 41130 682405 16.59141745684415 9.31501912432142 AADN04000906.1 41055 243779 5.9378638411886495 7.853335348497413 AADN04000908.1 41027 1541615 37.57562093255661 28.514168324731987 AADN04000907.1 41012 546589 13.327538281478592 14.314470092848328 AADN04000909.1 40979 464841 11.343395397642695 9.275991683869005 AADN04000910.1 40420 489641 12.113829787234042 9.635857465594064 AADN04000911.1 40390 1196120 29.6142609556821 22.821479082055273 AADN04000913.1 40021 167494 4.185152794782739 10.386965363101908 AADN04000914.1 39670 50010 1.2606503655155028 6.000407120993049 AADN04000915.1 39578 1177081 29.740790338066603 7.8948198051795115 AADN04000918.1 39432 3449 0.0874670318523027 0.5965847509550634 KQ759552.1 39391 421871 10.709832195171487 27.275787275952577 AADN04000922.1 39272 1375269 35.01907211244653 73.40728995900551 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