BamQC report ----------------------------------- >>>>>>> Input bam file = SRR7062655.recal.bam outfile = SRR7062655.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 = 374,090,624 number of mapped reads = 373,764,495 (99.91%) 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 = 31,696,579,295 bp number of sequenced bases = 31,674,407,044 bp number of aligned bases = 0 bp number of duplicated reads (flagged) = 19,739,099 >>>>>>> Insert size mean insert size = 28,831.7448 std insert size = 1,529,271.9878 median insert size = 477 >>>>>>> Mapping quality mean mapping quality = 7.6144 >>>>>>> ACTG content number of A's = 9,343,615,016 bp (29.5%) number of C's = 6,510,459,573 bp (20.55%) number of T's = 9,347,746,062 bp (29.51%) number of G's = 6,468,100,231 bp (20.42%) number of N's = 4,486,162 bp (0.01%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 261,967,938 number of insertions = 7,871,067 mapped reads with insertion percentage = 2.04% number of deletions = 8,613,160 mapped reads with deletion percentage = 2.22% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 25.7642X std coverageData = 27.3762X There is a 90.9% of reference with a coverageData >= 1X There is a 89.81% of reference with a coverageData >= 2X There is a 89.06% of reference with a coverageData >= 3X There is a 88.44% of reference with a coverageData >= 4X There is a 87.88% of reference with a coverageData >= 5X There is a 87.33% of reference with a coverageData >= 6X There is a 86.79% of reference with a coverageData >= 7X There is a 86.24% of reference with a coverageData >= 8X There is a 85.66% of reference with a coverageData >= 9X There is a 85.05% of reference with a coverageData >= 10X There is a 84.39% of reference with a coverageData >= 11X There is a 83.68% of reference with a coverageData >= 12X There is a 82.91% of reference with a coverageData >= 13X There is a 82.06% of reference with a coverageData >= 14X There is a 81.12% of reference with a coverageData >= 15X There is a 80.07% of reference with a coverageData >= 16X There is a 78.89% of reference with a coverageData >= 17X There is a 77.57% of reference with a coverageData >= 18X There is a 76.06% of reference with a coverageData >= 19X There is a 74.32% of reference with a coverageData >= 20X There is a 72.32% of reference with a coverageData >= 21X There is a 70.01% of reference with a coverageData >= 22X There is a 67.36% of reference with a coverageData >= 23X There is a 64.35% of reference with a coverageData >= 24X There is a 60.98% of reference with a coverageData >= 25X There is a 57.27% of reference with a coverageData >= 26X There is a 53.27% of reference with a coverageData >= 27X There is a 49.02% of reference with a coverageData >= 28X There is a 44.62% of reference with a coverageData >= 29X There is a 40.14% of reference with a coverageData >= 30X There is a 35.68% of reference with a coverageData >= 31X There is a 31.33% of reference with a coverageData >= 32X There is a 27.17% of reference with a coverageData >= 33X There is a 23.29% of reference with a coverageData >= 34X There is a 19.72% of reference with a coverageData >= 35X There is a 16.51% of reference with a coverageData >= 36X There is a 13.69% of reference with a coverageData >= 37X There is a 11.24% of reference with a coverageData >= 38X There is a 9.16% of reference with a coverageData >= 39X There is a 7.42% of reference with a coverageData >= 40X There is a 6% of reference with a coverageData >= 41X There is a 4.85% of reference with a coverageData >= 42X There is a 3.93% of reference with a coverageData >= 43X There is a 3.21% of reference with a coverageData >= 44X There is a 2.66% of reference with a coverageData >= 45X There is a 2.23% of reference with a coverageData >= 46X There is a 1.91% of reference with a coverageData >= 47X There is a 1.67% of reference with a coverageData >= 48X There is a 1.49% of reference with a coverageData >= 49X There is a 1.35% of reference with a coverageData >= 50X There is a 1.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig 1 196202544 5691482049 29.008197003806433 8.820170930191692 2 149560735 4349523097 29.081985301824037 8.90290306278254 3 111302122 3243680837 29.143027812174147 11.647733976801158 4 91282656 2653980372 29.07431146613438 9.139848212508358 5 59825302 1713442129 28.640760208782567 8.628353886391801 6 35467016 1000874827 28.219876941437644 8.989322018739244 7 36946936 1045120278 28.28706223433521 9.02922787523513 8 29963013 833546583 27.81918437241275 9.963308240533305 9 24091566 663140511 27.525836676619527 9.171712476433736 10 20435342 555663776 27.191312775680487 9.378284739939348 11 20218793 557977452 27.596971391912465 11.196121759733078 12 19948154 557053174 27.925048804014647 8.649848859978562 13 18407460 485244253 26.361282490903143 9.553802234836368 14 15595052 408555288 26.197750927666032 10.14635255381061 15 12762846 343946308 26.94902908019105 10.220997418590558 16 652338 9214529 14.125390518412233 24.110396791136104 17 10956400 272059049 24.83106211894418 12.151552724993303 18 11053727 290174063 26.251242047139396 8.791141990582553 19 9979828 261131549 26.165936827768977 8.647526755046034 20 14109371 377480616 26.75389399002975 12.062044836249369 21 6862722 178288668 25.97929334745018 15.595608154162472 22 4729743 108117022 22.85896337285134 13.123951057181824 23 5786528 138448512 23.926007443496342 9.9300015455559 24 6280547 157427680 25.06591862141944 7.793192947491963 25 2906300 43320477 14.905714138251385 14.512023789613126 26 5313770 122690624 23.08918602047134 10.464694254976054 27 5655794 121122542 21.41565658155159 12.747135135449632 28 4974273 111843857 22.48446295569222 37.07919950738868 30 24927 175536 7.042002647731375 8.105285876234296 31 49161 550717 11.202314843066658 12.537940993618477 32 78254 829341 10.59806527461855 9.175234902367746 33 1648031 27657675 16.78225409594844 11.770339735508731 W 5160035 4299918 0.8333117895518151 3.7668578231967595 Z 82310166 2469289140 29.999807557185584 12.580367090334635 MT 16775 190111 11.332995529061103 3.643452537640952 LGE64 897576 24450444 27.240527821599507 23.835358908981856 KQ759483.1 1265006 36622833 28.95071881081987 31.778010162195166 KQ759505.1 498515 5144501 10.31965136455272 8.043258218838302 KQ759404.1 476228 13679828 28.725375240431053 30.373886928567043 AADN04000541.1 371203 11193517 30.154705107447946 31.625318466993633 KQ759506.1 234913 3438280 14.636397304534018 5.02825691104884 KQ759543.1 226491 31977 0.14118441792389103 1.193922756018781 KQ759405.1 212434 4503032 21.197322462506 12.522771782260525 AADN04000593.1 209746 6417002 30.59415674196409 34.36469133158049 KQ759507.1 174450 2561101 14.681003152765836 5.361262524764096 AADN04000612.1 150454 2930461 19.47745490315977 10.277282384985028 KQ759527.1 143297 4516533 31.51868496898051 50.51087978526404 AADN04000623.1 140921 1553920 11.026887404999965 10.131922377293007 KQ759508.1 140174 2101497 14.992059868449212 5.27088940284716 AADN04000624.1 140122 3399973 24.264376757397127 14.860046226537586 AADN04000628.1 137062 2381582 17.37594665188017 22.669431766074773 AADN04000631.1 135147 3847573 28.46954057433757 9.513116089429534 KQ759484.1 129908 1525575 11.743503094497644 10.422057997052443 AADN04000639.1 125782 3495279 27.78838784563769 8.66758981776508 AADN04000640.1 125648 710970 5.65842671590475 7.3213580780709515 KQ759509.1 122550 1811494 14.781672786617706 5.389429007060814 AADN04000646.1 115712 46065 0.3981004563053097 1.6664046425374408 KQ759528.1 113001 1665562 14.7393562888824 14.228493088398686 KQ759510.1 111981 1578639 14.097382591689662 6.06894089890765 AADN04000659.1 99212 2082220 20.98758214732089 12.452907544089943 AADN04000661.1 96849 2006242 20.71515451889023 14.486649283767116 AADN04000662.1 96062 2085185 21.706658199912557 20.324707276553582 AADN04000668.1 90963 2167385 23.82710552642283 10.894815674236991 KQ759529.1 90829 15399 0.1695383632980656 0.8523180232615337 KQ759530.1 87745 2608430 29.727391874180864 46.53988151780318 AADN04000677.1 87083 2569853 29.510386642628298 80.15009029453697 AADN04000682.1 85355 2640369 30.9339698904575 29.724232251204146 KQ759486.1 84856 23004 0.2710945601960969 1.4496307009409908 KQ759511.1 84478 857234 10.147422997703544 6.695585583704697 KQ759531.1 84196 72350 0.8593044800228039 3.30912514903348 KQ759532.1 83724 2173754 25.963331900052555 14.40095772262005 KQ759480.1 81621 1398454 17.13350730816824 10.124257677624634 KQ759534.1 81551 650316 7.974347340927763 9.607766121688032 KQ759533.1 81163 1587779 19.562842674617745 21.906070820136573 AADN04000704.1 80105 2040282 25.4700954996567 10.683819656853203 AADN04000706.1 79378 1153572 14.53264128599864 12.6022277938733 AADN04000708.1 78622 847954 10.785200071226884 16.272578833185285 AADN04000710.1 77859 1225818 15.744075829383887 15.589001151110327 AADN04000712.1 77675 146269 1.8830897972320566 5.141216957235668 AADN04000711.1 77392 23547 0.3042562538763697 1.500509382630105 AADN04000717.1 76721 1013263 13.207114088711045 8.759206482825839 KQ759535.1 76388 988352 12.938576739802063 6.544583657098016 KQ759536.1 76109 594820 7.815370061359366 7.645733592668141 AADN04000729.1 74004 4913657 66.39718123344684 72.62636549443597 AADN04000732.1 73820 442546 5.994933622324574 7.3485400581190525 AADN04000736.1 70062 2590042 36.96785704090662 22.608354922614335 AADN04000737.1 69917 1013075 14.489680621308123 10.55732352261152 KQ759537.1 68154 2084363 30.58313525251636 60.64639984053357 AADN04000744.1 67341 1282453 19.044163288338456 10.254712223064292 AADN04000745.1 64791 925966 14.291583707613713 10.596265065885024 KQ759334.1 64707 468656 7.242740352666636 9.500018515917375 KQ759538.1 64595 803060 12.432231596872823 18.819751827222653 AADN04000750.1 64410 2029636 31.51119391398851 28.533481373081585 AADN04000751.1 64267 1962275 30.533166321751445 25.662197646525016 AADN04000752.1 64035 134644 2.102662606387132 5.335462363615519 AADN04000753.1 63752 870723 13.657971514619149 6.698778105148251 KQ759539.1 63582 706562 11.112610487244817 12.316101077832352 AADN04000754.1 63536 26114 0.41101108033240996 1.7055841851652702 KQ759487.1 63071 14791 0.23451348480284123 0.9945211493420203 KQ759540.1 63037 11197 0.17762583879308977 1.2733063062892171 AADN04000767.1 61976 2759966 44.532819155802244 68.11168456922891 KQ759541.1 60946 343323 5.633232697798051 12.200757583335546 KQ759466.1 60160 2563485 42.61112034574468 42.48530093166785 AADN04000772.1 60150 62037 1.0313715710723192 6.547215696227426 KQ759365.1 59978 50036 0.8342392210477175 2.6984078990881684 AADN04000776.1 59694 934462 15.654203102489362 7.410643597836765 AADN04000777.1 59540 853877 14.341232784682566 14.803294836553423 KQ759542.1 59175 9655 0.16316011829319815 1.0508781199524593 AADN04000780.1 59125 1971182 33.33923044397463 71.47725106199012 AADN04000785.1 57913 1861786 32.14798059157702 46.191619598793686 AADN04000787.1 57900 1793893 30.982607944732298 25.517336018156293 AADN04000789.1 57687 992889 17.211659472671485 28.67257022364568 AADN04000788.1 57649 79158 1.3731027424586724 10.50227041934826 AADN04000790.1 56914 487728 8.569561092174158 10.411107146140216 AADN04000792.1 56491 1557171 27.564939547892585 10.376217566497745 KQ759392.1 55852 1471526 26.346881042755854 12.23966001147731 AADN04000799.1 55430 1321068 23.83308677611402 10.971928566017592 AADN04000798.1 55229 42681 0.7728005214651723 2.3438190478286556 KQ759335.1 54779 5242 0.09569360521367677 0.6563731525835955 AADN04000801.1 53922 1205621 22.35861058566077 43.91374658158304 AADN04000802.1 53480 11177 0.20899401645474944 0.9560760489275595 AADN04000803.1 53392 618356 11.58143542103686 9.546704499252497 KQ759544.1 53158 720224 13.54874148764062 12.876682806536962 KQ759454.1 53068 267008 5.031431371071078 6.796790209548364 KQ759545.1 52844 6030 0.11410945424267656 0.656574408493319 KQ759481.1 52784 594287 11.258847377993332 11.369544297738335 AADN04000814.1 52690 2520229 47.831258303283356 48.617420422972856 AADN04000815.1 52096 245868 4.719517813267813 8.546299983004001 KQ759488.1 51788 25737 0.49696840967019384 2.1851004306463255 KQ759546.1 51687 687339 13.298102037262755 11.711009969337306 AADN04000827.1 51294 289400 5.641985417397747 8.09031352306044 AADN04000828.1 51194 29743 0.5809860530530921 1.6981578484899544 AADN04000829.1 50833 2449868 48.19444061928275 59.448149609441145 KQ759489.1 50595 9989 0.19743057614388773 1.055015773112733 AADN04000831.1 50160 159197 3.1737838915470493 6.0184104810201955 AADN04000832.1 50079 853089 17.03486491343677 15.518775478939697 AADN04000833.1 50010 639764 12.792721455708858 19.54618371951592 AADN04000834.1 49882 2440779 48.93105729521671 44.9184830972129 AADN04000835.1 49741 49217 0.9894654309322289 1.7369483486947082 AADN04000839.1 49566 573796 11.576403179598918 11.92735939090812 KQ759547.1 49554 1191332 24.041086491504217 27.870405079539772 AADN04000838.1 49481 216999 4.385501505628423 5.581390814646623 KQ759548.1 49166 59968 1.2197046739616808 4.423076318178822 AADN04000843.1 48646 42550 0.8746865107100276 4.144801388236976 KQ759549.1 47964 682367 14.226649153531815 8.981851784621492 AADN04000848.1 47841 1056492 22.08340126669593 11.059735038470544 AADN04000849.1 47738 265153 5.554338263018979 7.027605196343568 AADN04000850.1 47215 694100 14.7008365985386 9.598048474641901 KQ759455.1 46957 169034 3.599761483910812 5.606316706523591 KQ759513.1 46489 4092 0.08802082212996623 0.6956131386756615 AADN04000858.1 46233 756489 16.362533255466875 16.852173631607354 AADN04000861.1 45885 783212 17.06902037702953 17.962645517041793 AADN04000863.1 45565 290571 6.37706573027543 16.16988111036493 AADN04000864.1 45392 1460363 32.17225502291153 30.83671396949783 AADN04000865.1 45384 1094860 24.124361008284858 13.299457885179152 AADN04000866.1 45367 873906 19.26303260078912 24.054241988679767 AADN04000867.1 45304 433766 9.574562952498676 19.655706446284924 AADN04000868.1 45289 210092 4.63891894278964 8.878604940979683 AADN04000869.1 45021 1226687 27.2469958463828 24.69195577968914 AADN04000857.1 44988 99624 2.2144571885836224 4.686152236366297 KQ759514.1 44970 583130 12.96708917055815 7.05868903937308 AADN04000872.1 44775 454688 10.15495254048018 19.60477261380134 AADN04000873.1 44769 2241703 50.0726618865733 61.02467801873547 AADN04000874.1 44695 872420 19.519409329902675 18.40072465891964 AADN04000875.1 44461 208269 4.684307595420706 23.237011878913535 AADN04000876.1 44362 15729 0.3545602091880438 1.281410359569022 AADN04000877.1 44203 147922 3.3464244508291294 12.759920500176817 AADN04000879.1 43509 1654 0.03801512330782137 0.3036171821243382 KQ759550.1 43298 229288 5.295579472492956 6.151179280448226 AADN04000878.1 43025 557081 12.947844276583382 5.139460867377061 AADN04000886.1 42768 2832873 66.23814534231201 53.70994134187307 KQ759490.1 42671 62264 1.459164303625413 4.705992935710562 AADN04000890.1 42655 1915370 44.9037627476263 43.036355914814976 AADN04000891.1 42544 276451 6.498002068446785 5.762883800098901 AADN04000892.1 42175 591214 14.01811499703616 10.695392328691229 AADN04000894.1 42076 154761 3.6781300503850174 7.114984646648191 AADN04000895.1 42011 995934 23.70650543905168 18.15165230740917 AADN04000896.1 41836 444867 10.633593077732097 13.957121232829357 AADN04000898.1 41756 366618 8.780007663569307 7.640709608096534 AADN04000897.1 41744 638542 15.296617477960904 11.875388598762898 KQ759551.1 41656 578331 13.883498175532937 5.151442090000671 AADN04000901.1 41546 549459 13.225316516632168 56.69847104794025 AADN04000902.1 41531 396946 9.557824275842142 12.39321064870618 AADN04000903.1 41278 1728904 41.88439362372208 62.73185405843392 AADN04000905.1 41130 714464 17.370872842207636 10.177442743535256 AADN04000906.1 41055 259469 6.320034100596761 8.426509498171564 AADN04000908.1 41027 1224392 29.843566431861944 22.468471704268968 AADN04000907.1 41012 709653 17.303545303813518 18.830056823332278 AADN04000909.1 40979 431197 10.522389516581663 8.78911185952854 AADN04000910.1 40420 276411 6.838471053933696 8.701402181030783 AADN04000911.1 40390 722086 17.877841049764793 13.519523495596742 AADN04000913.1 40021 219024 5.4727268184203295 11.976458999534048 AADN04000914.1 39670 66958 1.687874968490043 6.878121528641299 AADN04000915.1 39578 1169231 29.54244782454899 7.320146109311426 AADN04000918.1 39432 5561 0.14102759180361127 0.7860722763460503 KQ759552.1 39391 423676 10.755654845015359 28.4176319245994 AADN04000922.1 39272 1488112 37.892442452638015 71.65210299079827 AADN04000923.1 39214 1241824 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