BamQC report ----------------------------------- >>>>>>> Input bam file = ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949270_hisat2.bam outfile = ../hcapsulatum/3-qualimap/genome/SRR949270/genome_results.txt >>>>>>> Reference number of bases = 30,483,324 bp number of contigs = 88 >>>>>>> Globals number of windows = 487 number of reads = 10,620,354 number of mapped reads = 10,258,051 (96.59%) number of mapped paired reads (first in pair) = 5,154,638 number of mapped paired reads (second in pair) = 5,103,413 number of mapped paired reads (both in pair) = 10,034,747 number of mapped paired reads (singletons) = 223,304 number of mapped bases = 1,073,605,293 bp number of sequenced bases = 798,526,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,596,515 duplication rate = 38.51% >>>>>>> Insert size mean insert size = 3,682.3316 std insert size = 32,270.4387 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 41.085 >>>>>>> ACTG content number of A's = 200,551,695 bp (25.12%) number of C's = 198,156,091 bp (24.82%) number of T's = 200,263,552 bp (25.08%) number of G's = 199,555,485 bp (24.99%) number of N's = 275,054,526 bp (34.45%) GC percentage = 49.81% >>>>>>> Mismatches and indels general error rate = 0.0009 number of mismatches = 915,854 number of insertions = 25,885 mapped reads with insertion percentage = 0.25% number of deletions = 19,638 mapped reads with deletion percentage = 0.19% homopolymer indels = 82.48% >>>>>>> Coverage mean coverageData = 35.2194X std coverageData = 104.727X There is a 76.2% of reference with a coverageData >= 1X There is a 69.53% of reference with a coverageData >= 2X There is a 64.66% of reference with a coverageData >= 3X There is a 60.85% of reference with a coverageData >= 4X There is a 57.7% of reference with a coverageData >= 5X There is a 55% of reference with a coverageData >= 6X There is a 52.61% of reference with a coverageData >= 7X There is a 50.45% of reference with a coverageData >= 8X There is a 48.47% of reference with a coverageData >= 9X There is a 46.66% of reference with a coverageData >= 10X There is a 44.97% of reference with a coverageData >= 11X There is a 43.39% of reference with a coverageData >= 12X There is a 41.88% of reference with a coverageData >= 13X There is a 40.43% of reference with a coverageData >= 14X There is a 39.04% of reference with a coverageData >= 15X There is a 37.69% of reference with a coverageData >= 16X There is a 36.41% of reference with a coverageData >= 17X There is a 35.17% of reference with a coverageData >= 18X There is a 33.98% of reference with a coverageData >= 19X There is a 32.83% of reference with a coverageData >= 20X There is a 31.72% of reference with a coverageData >= 21X There is a 30.65% of reference with a coverageData >= 22X There is a 29.62% of reference with a coverageData >= 23X There is a 28.63% of reference with a coverageData >= 24X There is a 27.68% of reference with a coverageData >= 25X There is a 26.76% of reference with a coverageData >= 26X There is a 25.87% of reference with a coverageData >= 27X There is a 25.02% of reference with a coverageData >= 28X There is a 24.19% of reference with a coverageData >= 29X There is a 23.4% of reference with a coverageData >= 30X There is a 22.64% of reference with a coverageData >= 31X There is a 21.9% of reference with a coverageData >= 32X There is a 21.19% of reference with a coverageData >= 33X There is a 20.51% of reference with a coverageData >= 34X There is a 19.86% of reference with a coverageData >= 35X There is a 19.23% of reference with a coverageData >= 36X There is a 18.63% of reference with a coverageData >= 37X There is a 18.04% of reference with a coverageData >= 38X There is a 17.48% of reference with a coverageData >= 39X There is a 16.94% of reference with a coverageData >= 40X There is a 16.42% of reference with a coverageData >= 41X There is a 15.93% of reference with a coverageData >= 42X There is a 15.45% of reference with a coverageData >= 43X There is a 14.99% of reference with a coverageData >= 44X There is a 14.55% of reference with a coverageData >= 45X There is a 14.13% of reference with a coverageData >= 46X There is a 13.72% of reference with a coverageData >= 47X There is a 13.32% of reference with a coverageData >= 48X There is a 12.94% of reference with a coverageData >= 49X There is a 12.58% of reference with a coverageData >= 50X There is a 12.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig GG663448.1 2407 79598 33.06938097216452 33.52739001337234 GG663447.1 5093 535 0.1050461417632044 0.3955377240367899 GG663446.1 5267 1696 0.32200493639643063 1.272295347950055 GG663445.1 5726 3429 0.5988473629060426 2.0378685450440743 GG663444.1 6104 0 0.0 0.0 GG663443.1 6704 0 0.0 0.0 GG663442.1 7013 0 0.0 0.0 GG663441.1 7428 0 0.0 0.0 GG663440.1 7433 0 0.0 0.0 GG663439.1 7612 0 0.0 0.0 GG663438.1 9352 10089 1.0788066723695466 3.857532060308578 GG663437.1 9532 96522 10.126101552664709 7.9103187383462075 GG663436.1 9723 848578 87.27532654530495 99.8290906055757 GG663435.1 10315 0 0.0 0.0 GG663434.1 11106 142068 12.792004321988115 25.96426213348737 GG663433.1 11483 0 0.0 0.0 GG663432.1 11832 0 0.0 0.0 GG663431.1 11849 1202 0.10144315976031733 0.5782535285599093 GG663430.1 11959 0 0.0 0.0 GG663429.1 12280 0 0.0 0.0 GG663428.1 12330 161309 13.08264395782644 28.536657719190963 GG663427.1 12422 2079 0.16736435356625343 0.7420014767804263 GG663426.1 14805 156 0.010536980749746707 0.1208872498941329 GG663425.1 15274 3111 0.20367945528348827 1.0603904643662272 GG663424.1 15855 0 0.0 0.0 GG663423.1 16334 102329 6.264785110811804 15.377480053303 GG663422.1 16757 244451 14.587993077519842 22.08864996287776 GG663421.1 17071 78 0.004569152363657665 0.06744090161271087 GG663420.1 17227 1363 0.07911998606838103 0.4386143724116335 GG663419.1 17524 24357 1.3899223921479114 4.020314861714722 GG663418.1 17580 312 0.017747440273037544 0.18013754046064048 GG663417.1 18806 0 0.0 0.0 GG663416.1 20314 3881 0.19105050703948015 1.0276219308797714 GG663415.1 20172 16089 0.7975907198096371 1.4243565159564455 GG663414.1 21124 892 0.042226850975194095 0.2554838713496152 GG663413.1 21814 23475 1.0761437608875035 3.764474620819833 GG663412.1 22664 78 0.003441581362513237 0.05856395546954149 GG663411.1 23942 0 0.0 0.0 GG663410.1 24438 0 0.0 0.0 GG663409.1 30061 23504 0.7818768504041782 0.7832807640622307 GG663408.1 29608 389 0.013138340988921913 0.15636210491828081 GG663407.1 31202 1193565 38.252836356643805 52.94386924008807 GG663406.1 31468 0 0.0 0.0 GG663405.1 33416 312 0.009336844625329183 0.1084593648258978 GG663404.1 33436 234 0.006998444790046656 0.09189592344862056 GG663403.1 34148 3161 0.09256764671430245 0.973330011964636 GG663402.1 35232 201804 5.727861035422343 9.57687446822198 GG663401.1 36230 1203413 33.21592602815346 41.84102717903652 GG663400.1 40055 0 0.0 0.0 GG663399.1 47125 2846 0.060392572944297084 0.36735476156399627 GG663398.1 49169 0 0.0 0.0 GG663397.1 50304 6308 0.12539758269720103 0.535467520519121 GG663396.1 51171 56372 1.1016396005550018 1.3501638557130173 GG663395.1 53466 77185 1.4436277260314967 3.540519160955723 GG663394.1 53864 79903 1.483421208970741 6.927439674796805 GG663393.1 55852 440407 7.885250304375851 45.92367050828009 GG663392.1 60589 7780 0.12840614633019196 0.8220170154076561 GG663391.1 76172 4269 0.05604421572231266 0.4276082250157953 GG663390.1 87620 20851 0.23797078292627255 2.449405832726917 GG663389.1 88906 389 0.004375407734011203 0.08585268350713009 GG663388.1 95026 64557 0.6793614379222529 0.8659631712202445 GG663387.1 113334 294995 2.602881747754425 13.636895910885556 GG663386.1 144210 76521 0.530622009569378 1.113413143295548 GG663385.1 156336 115052 0.7359277453689489 4.131637438270087 GG663384.1 204511 4162604 20.35393695204659 32.38792400179542 GG663383.1 258077 7185685 27.843182461048446 64.02115173843578 GG663382.1 261570 5768864 22.05476163168559 32.24619453738942 GG663381.1 280411 5766654 20.565006365656128 27.683914929456524 GG663380.1 351122 14954643 42.59101679758033 74.65121799043354 GG663379.1 441739 18170640 41.134334980610724 109.05420380411364 GG663378.1 530530 17152458 32.33079750438241 63.44571358737887 GG663377.1 695743 21367472 30.711731199595253 49.1167893699683 GG663376.1 920403 26006518 28.255577176519417 54.92240709242052 GG663375.1 915096 24804080 27.105440303530997 47.211681700869235 GG663374.1 967551 26133602 27.010051149758514 53.12852856126154 GG663373.1 1058542 64766426 61.18455951676929 267.4083122586951 GG663372.1 1221551 51658866 42.289569571798474 119.88193959385457 GG663371.1 1250234 33644670 26.910698317275006 43.08714378534432 GG663370.1 1327755 54019198 40.6846127485869 276.49846727705284 GG663369.1 1498222 62922738 41.99827395406021 68.25490356768363 GG663368.1 1769553 50949791 28.79246397253996 51.902049047974 GG663367.1 2225114 85888653 38.59966410709743 104.40967322938407 GG663366.1 2702831 173075146 64.03476428973917 81.82848505605716 GG663365.1 2818386 100944920 35.81657019301118 105.58559093839926 GG663364.1 2928037 92245858 31.504334815441197 51.26404287494866 GG663363.1 3777229 126284843 33.43319745771305 77.35379705116456 GG663450.1 4245 5818 1.3705535924617196 4.838641583023251 GG663449.1 40201 83652 2.08084376010547 6.785792227129246