BamQC report ----------------------------------- >>>>>>> Input bam file = SRR7062654_1.bam outfile = SRR7062654_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 = 371,799,352 number of mapped reads = 370,874,029 (99.75%) 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 = 33,209,980,887 bp number of sequenced bases = 33,186,798,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,115,539 duplication rate = 19.71% >>>>>>> Insert size mean insert size = 28,493.2379 std insert size = 1,522,158.3522 median insert size = 479 >>>>>>> Mapping quality mean mapping quality = 7.6381 >>>>>>> ACTG content number of A's = 9,799,698,394 bp (29.53%) number of C's = 6,798,168,718 bp (20.48%) number of T's = 9,790,239,890 bp (29.5%) number of G's = 6,792,037,700 bp (20.47%) number of N's = 6,653,492 bp (0.02%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 275,451,374 number of insertions = 8,138,082 mapped reads with insertion percentage = 2.13% number of deletions = 8,940,579 mapped reads with deletion percentage = 2.33% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 26.9943X std coverageData = 26.1098X There is a 90.77% of reference with a coverageData >= 1X There is a 89.7% of reference with a coverageData >= 2X There is a 88.98% of reference with a coverageData >= 3X There is a 88.37% of reference with a coverageData >= 4X There is a 87.82% of reference with a coverageData >= 5X There is a 87.3% of reference with a coverageData >= 6X There is a 86.78% of reference with a coverageData >= 7X There is a 86.25% of reference with a coverageData >= 8X There is a 85.7% of reference with a coverageData >= 9X There is a 85.12% of reference with a coverageData >= 10X There is a 84.51% of reference with a coverageData >= 11X There is a 83.85% of reference with a coverageData >= 12X There is a 83.14% of reference with a coverageData >= 13X There is a 82.37% of reference with a coverageData >= 14X There is a 81.54% of reference with a coverageData >= 15X There is a 80.62% of reference with a coverageData >= 16X There is a 79.62% of reference with a coverageData >= 17X There is a 78.51% of reference with a coverageData >= 18X There is a 77.27% of reference with a coverageData >= 19X There is a 75.86% of reference with a coverageData >= 20X There is a 74.26% of reference with a coverageData >= 21X There is a 72.42% of reference with a coverageData >= 22X There is a 70.31% of reference with a coverageData >= 23X There is a 67.91% of reference with a coverageData >= 24X There is a 65.2% of reference with a coverageData >= 25X There is a 62.16% of reference with a coverageData >= 26X There is a 58.81% of reference with a coverageData >= 27X There is a 55.17% of reference with a coverageData >= 28X There is a 51.3% of reference with a coverageData >= 29X There is a 47.25% of reference with a coverageData >= 30X There is a 43.08% of reference with a coverageData >= 31X There is a 38.87% of reference with a coverageData >= 32X There is a 34.71% of reference with a coverageData >= 33X There is a 30.65% of reference with a coverageData >= 34X There is a 26.78% of reference with a coverageData >= 35X There is a 23.15% of reference with a coverageData >= 36X There is a 19.8% of reference with a coverageData >= 37X There is a 16.77% of reference with a coverageData >= 38X There is a 14.06% of reference with a coverageData >= 39X There is a 11.69% of reference with a coverageData >= 40X There is a 9.65% of reference with a coverageData >= 41X There is a 7.92% of reference with a coverageData >= 42X There is a 6.46% of reference with a coverageData >= 43X There is a 5.27% of reference with a coverageData >= 44X There is a 4.3% of reference with a coverageData >= 45X There is a 3.51% of reference with a coverageData >= 46X There is a 2.89% of reference with a coverageData >= 47X There is a 2.41% of reference with a coverageData >= 48X There is a 2.03% of reference with a coverageData >= 49X There is a 1.74% of reference with a coverageData >= 50X There is a 1.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig 1 196202544 6007518147 30.618961530896357 9.507032963295979 2 149560735 4589335233 30.685428451525063 10.569486513040681 3 111302122 3427374085 30.7934298413466 13.772429791644482 4 91282656 2801052912 30.685488730739824 9.835559914637553 5 59825302 1817755451 30.38439239303798 9.173796749768302 6 35467016 1064233298 30.006282400526732 9.681567261038948 7 36946936 1106443142 29.946817294944296 9.378635726702191 8 29963013 886481079 29.585845689150155 11.053983344557114 9 24091566 707230701 29.35594560353611 9.81811368831765 10 20435342 593365178 29.036224497735343 10.37642234622559 11 20218793 592765897 29.317570885660682 12.18251372948578 12 19948154 592519261 29.702962038492384 9.194178430869872 13 18407460 517100611 28.091904640835835 10.249543922595937 14 15595052 438599245 28.124256655251934 11.905080569095409 15 12762846 367535729 28.79731754187115 9.454195048224967 16 652338 9986985 15.309525123478933 18.928914356486487 17 10956400 289434798 26.416961593224052 11.191385055952248 18 11053727 311436049 28.17475490393421 9.782332618664325 19 9979828 281367629 28.19363510072518 9.69007255523533 20 14109371 404781522 28.68884247214139 13.030368394200432 21 6862722 188821501 27.514082750255657 10.908951594861067 22 4729743 115459171 24.411299091726548 13.18062229468136 23 5786528 150019782 25.925698795547174 10.081848978431594 24 6280547 169126744 26.928664652935485 8.277629301837063 25 2906300 46909860 16.140749406461826 14.212783679488652 26 5313770 132590549 24.952255931287954 10.015960564705205 27 5655794 131597230 23.26768443122221 13.909712006771766 28 4974273 120278069 24.180029724946742 25.567498527781012 30 24927 180055 7.223292012677017 8.852464613057089 31 49161 593435 12.071255670145034 15.501951288647769 32 78254 966719 12.35360492754364 10.65026051670644 33 1648031 29910212 18.14905908930111 12.911624108543752 W 5160035 4221324 0.8180804975160052 4.152277721021582 Z 82310166 2575176282 31.28624818956142 12.884225392097305 MT 16775 446600 26.62295081967213 6.928085942446633 LGE64 897576 22438831 24.99936607039404 19.388855020378948 KQ759483.1 1265006 43235606 34.178182554074844 34.605667635458566 KQ759505.1 498515 5472193 10.976987653330392 8.651486708835348 KQ759404.1 476228 18228901 38.27767581914545 35.4121381137987 AADN04000541.1 371203 14301658 38.52786211318335 37.79796650947127 KQ759506.1 234913 3568288 15.189827723455066 5.223725738796117 KQ759543.1 226491 32926 0.14537442988904636 1.259049762307736 KQ759405.1 212434 4927551 23.195679599310846 14.731059674574098 AADN04000593.1 209746 7073227 33.72282188933281 34.75926545326669 KQ759507.1 174450 2584705 14.816308397821725 5.5399116783419 AADN04000612.1 150454 3199257 21.264020896752495 11.073420286553734 KQ759527.1 143297 4033853 28.150296237883556 33.03685458877369 AADN04000623.1 140921 1730243 12.278106172962156 10.745625906598383 KQ759508.1 140174 2147971 15.323604948135888 5.668362556451377 AADN04000624.1 140122 3993667 28.50135596123378 23.99193891544775 AADN04000628.1 137062 3864905 28.19822416132845 26.96820029026349 AADN04000631.1 135147 3986928 29.50067704055584 10.692154843119216 KQ759484.1 129908 1657343 12.757820919419897 11.529956858649347 AADN04000639.1 125782 3647856 29.00141514684136 9.435270198177557 AADN04000640.1 125648 1627167 12.950202152043804 14.714498289326594 KQ759509.1 122550 1859196 15.170917992656058 5.344223182289998 AADN04000646.1 115712 52887 0.4570571764380531 1.894813303828886 KQ759528.1 113001 2789841 24.6886399235405 21.981420438358793 KQ759510.1 111981 1647907 14.715951813254033 6.554173245540631 AADN04000659.1 99212 2297565 23.15813611256703 14.134986147942895 AADN04000661.1 96849 2207845 22.796776425156686 14.424651511677936 AADN04000662.1 96062 2101755 21.87915096500177 18.038925074800243 AADN04000668.1 90963 2280260 25.067994679155262 11.60419641784472 KQ759529.1 90829 13398 0.14750795450792148 0.8617745086466237 KQ759530.1 87745 2942281 33.53217847170779 136.3109181047738 AADN04000677.1 87083 2427080 27.87088180241838 95.64025246266633 AADN04000682.1 85355 3360705 39.37326460078496 32.775434081838235 KQ759486.1 84856 22331 0.2631634769491845 1.9737840022790238 KQ759511.1 84478 895018 10.59468737422761 6.709427802371572 KQ759531.1 84196 64199 0.7624946553280441 2.778693833373601 KQ759532.1 83724 2139663 25.556148774544933 13.918280084721898 KQ759480.1 81621 1497164 18.34287744575538 10.463074255423294 KQ759534.1 81551 711464 8.724160341381467 10.424785078805943 KQ759533.1 81163 2225742 27.423111516331332 26.641301263472446 AADN04000704.1 80105 2141952 26.739304662630296 11.340842276455584 AADN04000706.1 79378 1249520 15.741389301821663 13.195328153299796 AADN04000708.1 78622 794142 10.100760601358399 14.218228526989877 AADN04000710.1 77859 1292634 16.60224251531615 16.117878031991687 AADN04000712.1 77675 134070 1.726037978757644 4.932559957879667 AADN04000711.1 77392 24194 0.3126162910895183 1.6354764141814562 AADN04000717.1 76721 1063796 13.865773386686826 8.378437863989566 KQ759535.1 76388 1014946 13.286720427292245 6.687105104278741 KQ759536.1 76109 630953 8.290123375684873 8.654179481000586 AADN04000729.1 74004 3966505 53.59852170152965 67.66281821285963 AADN04000732.1 73820 460769 6.241790842590084 8.01939633678404 AADN04000736.1 70062 1368933 19.538879849276356 16.559636685691746 AADN04000737.1 69917 1126025 16.10516755581618 11.790471223215008 KQ759537.1 68154 5510715 80.85680957830795 373.49306122064365 AADN04000744.1 67341 1393457 20.692549858184464 11.027723850588345 AADN04000745.1 64791 978010 15.094843419610749 10.922667452960729 KQ759334.1 64707 838171 12.953328078878638 16.06604677580779 KQ759538.1 64595 596303 9.231411099930336 13.235641725110616 AADN04000750.1 64410 2642678 41.02900170780935 37.693861672506756 AADN04000751.1 64267 1952832 30.38623243655375 24.44087817949152 AADN04000752.1 64035 156536 2.444538143202936 5.858954757558613 AADN04000753.1 63752 862880 13.53494792320241 6.621525713193504 KQ759539.1 63582 771117 12.127913560441634 14.532011195059944 AADN04000754.1 63536 31411 0.4943811382523294 2.206184465956233 KQ759487.1 63071 16897 0.267904425171632 1.426422253288166 KQ759540.1 63037 7028 0.1114900772562146 0.8803518234479261 AADN04000767.1 61976 1789998 28.88211565767394 50.90776051421706 KQ759541.1 60946 348281 5.714583401699866 10.561297625316286 KQ759466.1 60160 2281821 37.92920545212766 40.70875441765323 AADN04000772.1 60150 76136 1.265768911055694 8.979517325417286 KQ759365.1 59978 68344 1.139484477641802 4.001150935765698 AADN04000776.1 59694 1048502 17.564612858913794 8.340395702227491 AADN04000777.1 59540 892578 14.991232784682566 15.38864127953186 KQ759542.1 59175 12453 0.21044359949302915 1.7451199660104255 AADN04000780.1 59125 1993546 33.7174799154334 86.17074268187466 AADN04000785.1 57913 1760379 30.39695750522335 41.30887705446352 AADN04000787.1 57900 1243359 21.47424870466321 18.687251069170536 AADN04000789.1 57687 1052853 18.251131104061574 34.11013522881114 AADN04000788.1 57649 74470 1.291783031795868 10.059576548701177 AADN04000790.1 56914 535473 9.408458375795059 10.947488815609015 AADN04000792.1 56491 1579975 27.968614469561523 10.671283804912774 KQ759392.1 55852 1517188 27.164434577096614 13.87374961324148 AADN04000799.1 55430 1394208 25.152588850802815 11.589516025546537 AADN04000798.1 55229 46964 0.8503503594126274 3.1461398747701166 KQ759335.1 54779 5331 0.09731831541284068 0.7851948354116692 AADN04000801.1 53922 1453052 26.9472942398279 82.61246779495224 AADN04000802.1 53480 11884 0.22221391174270755 0.9444514100258297 AADN04000803.1 53392 569346 10.663507641594247 8.06726031567962 KQ759544.1 53158 615363 11.57611272056887 11.775859885450393 KQ759454.1 53068 302593 5.701986131001734 7.663547158793736 KQ759545.1 52844 7368 0.1394292634925441 0.70058267522598 KQ759481.1 52784 651446 12.341732343134282 12.585852222779373 AADN04000814.1 52690 3016972 57.25891060922376 63.52618998906427 AADN04000815.1 52096 205849 3.9513398341523343 7.345293672533455 KQ759488.1 51788 22716 0.438634432687109 2.000709248278948 KQ759546.1 51687 763738 14.776210652581888 15.626641173403245 AADN04000827.1 51294 399010 7.778882520372753 10.654476880593986 AADN04000828.1 51194 49156 0.9601906473414853 2.961441122777666 AADN04000829.1 50833 2409361 47.39757637755002 68.98245376835465 KQ759489.1 50595 9336 0.1845241624666469 0.7933834192927283 AADN04000831.1 50160 165446 3.298365231259968 7.1461002680502075 AADN04000832.1 50079 761643 15.208830048523334 12.736357711686342 AADN04000833.1 50010 531754 10.632953409318135 16.06015194252825 AADN04000834.1 49882 1719710 34.475562327091936 33.85484871271812 AADN04000835.1 49741 46138 0.9275647855893528 1.7679707588285094 AADN04000839.1 49566 757586 15.284388492111528 17.29477455753694 KQ759547.1 49554 1265913 25.546131492916818 27.988300243072754 AADN04000838.1 49481 392989 7.94222024615509 7.297786667951304 KQ759548.1 49166 53834 1.0949436602530205 4.347444673505058 AADN04000843.1 48646 32684 0.671874357603914 3.3671484644919634 KQ759549.1 47964 729446 15.208197815027937 10.199306122490322 AADN04000848.1 47841 1047168 21.8885056750486 13.436113451723635 AADN04000849.1 47738 273196 5.722820394654154 7.891162728146611 AADN04000850.1 47215 694063 14.700052949274594 9.62138730758336 KQ759455.1 46957 215563 4.590646761931128 6.511208244776109 KQ759513.1 46489 3357 0.07221063047172449 0.44227192263323895 AADN04000858.1 46233 563709 12.192784374797222 13.717835656224656 AADN04000861.1 45885 640409 13.956826849733028 12.423219184014075 AADN04000863.1 45565 211097 4.632876111050148 10.871803934765465 AADN04000864.1 45392 1260398 27.766963341557982 24.34339883285476 AADN04000865.1 45384 1067004 23.51057641459545 12.809012461729862 AADN04000866.1 45367 1796547 39.60030418586197 43.400994284007794 AADN04000867.1 45304 369935 8.165614515274589 15.97036044978284 AADN04000868.1 45289 181685 4.011680540528605 8.708063080903429 AADN04000869.1 45021 1199550 26.644232691410675 23.686193858828208 AADN04000857.1 44988 100551 2.2350626833822353 4.843433951368088 KQ759514.1 44970 557582 12.398977095841673 6.772123066770573 AADN04000872.1 44775 567811 12.68142936906756 25.60217083315353 AADN04000873.1 44769 2470368 55.180325671781816 120.09713382214726 AADN04000874.1 44695 736001 16.46718872357087 16.45535040161722 AADN04000875.1 44461 166589 3.746856795843548 11.495269135774258 AADN04000876.1 44362 17361 0.3913484513773049 1.3851526872417712 AADN04000877.1 44203 126339 2.8581544239078798 10.957928999143503 AADN04000879.1 43509 1296 0.029786940632972488 0.32987201833454444 KQ759550.1 43298 249758 5.768349577347683 6.882822313244217 AADN04000878.1 43025 578182 13.438280069726902 5.631462706399272 AADN04000886.1 42768 2611528 61.062663673774786 56.419987089338186 KQ759490.1 42671 48114 1.1275573574558835 3.7494204001293236 AADN04000890.1 42655 818638 19.19207595826984 17.997769874882355 AADN04000891.1 42544 312274 7.34002444528018 8.13598198992356 AADN04000892.1 42175 394350 9.350326022525193 10.80469682599396 AADN04000894.1 42076 177165 4.210595113603954 7.184567520308665 AADN04000895.1 42011 740327 17.62221799052629 16.924240186138036 AADN04000896.1 41836 476550 11.390907352519362 13.399104041656217 AADN04000898.1 41756 228032 5.4610594884567485 9.15101675238967 AADN04000897.1 41744 256495 6.1444758528171715 7.074794531795618 KQ759551.1 41656 594459 14.270669291338583 5.589071342369996 AADN04000901.1 41546 299244 7.202715062821932 21.36200930223668 AADN04000902.1 41531 267777 6.447641520791698 8.174404087141236 AADN04000903.1 41278 1523011 36.896433935752704 60.87755375214895 AADN04000905.1 41130 699289 17.001920739119864 9.679259395512265 AADN04000906.1 41055 250149 6.093021556448666 8.157299467828706 AADN04000908.1 41027 1592524 38.816486703877935 29.599820045370507 AADN04000907.1 41012 561826 13.699063688676485 14.835222995313638 AADN04000909.1 40979 470040 11.470265257814978 9.37639782513703 AADN04000910.1 40420 502270 12.426274121721919 9.915880988517516 AADN04000911.1 40390 1207803 29.903515721713294 23.102199991254626 AADN04000913.1 40021 171833 4.293570875290473 10.709055158591312 AADN04000914.1 39670 50367 1.2696496092765315 6.055844282771129 AADN04000915.1 39578 1223940 30.924756177674464 8.361852295942976 AADN04000918.1 39432 3449 0.0874670318523027 0.5965847509550634 KQ759552.1 39391 436686 11.085933335025768 29.346841024592923 AADN04000922.1 39272 2077691 52.905148706457524 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