BamQC report ----------------------------------- >>>>>>> Input bam file = ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949916_hisat2.bam outfile = ../hcapsulatum/3-qualimap/genome/SRR949916/genome_results.txt >>>>>>> Reference number of bases = 30,483,324 bp number of contigs = 88 >>>>>>> Globals number of windows = 487 number of reads = 16,489,196 number of mapped reads = 15,585,452 (94.52%) number of mapped paired reads (first in pair) = 7,739,837 number of mapped paired reads (second in pair) = 7,845,615 number of mapped paired reads (both in pair) = 14,864,764 number of mapped paired reads (singletons) = 720,688 number of mapped bases = 3,032,517,271 bp number of sequenced bases = 1,244,075,683 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,239,033 duplication rate = 42.65% >>>>>>> Insert size mean insert size = 2,332.6774 std insert size = 27,472.1768 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 38.7096 >>>>>>> ACTG content number of A's = 319,449,327 bp (25.68%) number of C's = 303,652,491 bp (24.41%) number of T's = 317,021,195 bp (25.48%) number of G's = 303,952,670 bp (24.43%) number of N's = 1,788,396,958 bp (143.75%) GC percentage = 48.84% >>>>>>> Mismatches and indels general error rate = 0.0014 number of mismatches = 3,986,740 number of insertions = 110,756 mapped reads with insertion percentage = 0.71% number of deletions = 37,011 mapped reads with deletion percentage = 0.23% homopolymer indels = 86.9% >>>>>>> Coverage mean coverageData = 99.4812X std coverageData = 293.7997X There is a 76.15% of reference with a coverageData >= 1X There is a 69.63% of reference with a coverageData >= 2X There is a 65.06% of reference with a coverageData >= 3X There is a 61.53% of reference with a coverageData >= 4X There is a 58.59% of reference with a coverageData >= 5X There is a 56.06% of reference with a coverageData >= 6X There is a 53.8% of reference with a coverageData >= 7X There is a 51.77% of reference with a coverageData >= 8X There is a 49.91% of reference with a coverageData >= 9X There is a 48.19% of reference with a coverageData >= 10X There is a 46.57% of reference with a coverageData >= 11X There is a 45.04% of reference with a coverageData >= 12X There is a 43.59% of reference with a coverageData >= 13X There is a 42.23% of reference with a coverageData >= 14X There is a 40.93% of reference with a coverageData >= 15X There is a 39.69% of reference with a coverageData >= 16X There is a 38.51% of reference with a coverageData >= 17X There is a 37.37% of reference with a coverageData >= 18X There is a 36.28% of reference with a coverageData >= 19X There is a 35.23% of reference with a coverageData >= 20X There is a 34.23% of reference with a coverageData >= 21X There is a 33.28% of reference with a coverageData >= 22X There is a 32.36% of reference with a coverageData >= 23X There is a 31.48% of reference with a coverageData >= 24X There is a 30.64% of reference with a coverageData >= 25X There is a 29.82% of reference with a coverageData >= 26X There is a 29.03% of reference with a coverageData >= 27X There is a 28.28% of reference with a coverageData >= 28X There is a 27.55% of reference with a coverageData >= 29X There is a 26.85% of reference with a coverageData >= 30X There is a 26.17% of reference with a coverageData >= 31X There is a 25.51% of reference with a coverageData >= 32X There is a 24.88% of reference with a coverageData >= 33X There is a 24.27% of reference with a coverageData >= 34X There is a 23.68% of reference with a coverageData >= 35X There is a 23.12% of reference with a coverageData >= 36X There is a 22.57% of reference with a coverageData >= 37X There is a 22.04% of reference with a coverageData >= 38X There is a 21.52% of reference with a coverageData >= 39X There is a 21.02% of reference with a coverageData >= 40X There is a 20.55% of reference with a coverageData >= 41X There is a 20.09% of reference with a coverageData >= 42X There is a 19.64% of reference with a coverageData >= 43X There is a 19.21% of reference with a coverageData >= 44X There is a 18.8% of reference with a coverageData >= 45X There is a 18.4% of reference with a coverageData >= 46X There is a 18.01% of reference with a coverageData >= 47X There is a 17.63% of reference with a coverageData >= 48X There is a 17.27% of reference with a coverageData >= 49X There is a 16.92% of reference with a coverageData >= 50X There is a 16.58% of reference with a coverageData >= 51X >>>>>>> Coverage per contig GG663448.1 2407 153100 63.606148732862486 64.32204966482732 GG663447.1 5093 80 0.015707834282348322 0.12434266453839006 GG663446.1 5267 319 0.06056578697550788 0.2947807215703454 GG663445.1 5726 877 0.15316101990918618 0.6555437821277468 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 160 0.021019442984760904 0.14344903625110658 GG663438.1 9352 17080 1.8263473053892216 6.2577190926300394 GG663437.1 9532 77152 8.09399916072178 6.568722917237168 GG663436.1 9723 336561 34.614933662449864 41.37291782723828 GG663435.1 10315 0 0.0 0.0 GG663434.1 11106 247527 22.287682333873583 47.77701600156459 GG663433.1 11483 160 0.013933641034572846 0.12230571643475067 GG663432.1 11832 0 0.0 0.0 GG663431.1 11849 557 0.04700818634483923 0.21004503482958203 GG663430.1 11959 320 0.026758090141316162 0.22978290818644784 GG663429.1 12280 0 0.0 0.0 GG663428.1 12330 828995 67.23398215733982 156.5408966883837 GG663427.1 12422 1997 0.16076316213170183 0.8825122134820903 GG663426.1 14805 0 0.0 0.0 GG663425.1 15274 531 0.0347649600628519 0.18583866569420407 GG663424.1 15855 160 0.010091453800063072 0.09994806831682272 GG663423.1 16334 170122 10.415207542549284 25.132061279092717 GG663422.1 16757 212211 12.664021006146685 18.74369772807577 GG663421.1 17071 0 0.0 0.0 GG663420.1 17227 316 0.0183432983107912 0.14659374632100722 GG663419.1 17524 4152 0.23693220725861674 1.0832779273992026 GG663418.1 17580 227 0.012912400455062572 0.11878913284834287 GG663417.1 18806 0 0.0 0.0 GG663416.1 20314 1315 0.06473368120508025 0.2811709147543487 GG663415.1 20172 3175 0.1573963910370811 0.7260371924914645 GG663414.1 21124 80 0.0037871615224389322 0.061423276777146055 GG663413.1 21814 16831 0.7715687173374897 2.5636176973642546 GG663412.1 22664 637 0.0281062477938581 0.18410070543809323 GG663411.1 23942 1200 0.05012112605463203 0.2737243366553697 GG663410.1 24438 0 0.0 0.0 GG663409.1 30061 80 0.002661255447257244 0.05151866813788655 GG663408.1 29608 1564 0.05282356119967576 0.27685337071481086 GG663407.1 31202 3828975 122.71569130183963 186.90875499648152 GG663406.1 31468 0 0.0 0.0 GG663405.1 33416 160 0.004788125448886761 0.08531685158418607 GG663404.1 33436 640 0.019141045579614786 0.1852748377065027 GG663403.1 34148 2027 0.05935925969310062 0.44423355508669277 GG663402.1 35232 36550 1.0374091734786557 2.109180880151623 GG663401.1 36230 1917630 52.929340325696934 80.24633160769122 GG663400.1 40055 160 0.0039945075521158405 0.06540748831701626 GG663399.1 47125 80 0.0016976127320954908 0.04116710875331565 GG663398.1 49169 640 0.013016331428338994 0.1468045577875167 GG663397.1 50304 3346 0.06651558524173028 0.35460435979209753 GG663396.1 51171 4140 0.08090520021105704 0.5124334717066965 GG663395.1 53466 64944 1.2146784872629335 1.2438658287897189 GG663394.1 53864 207762 3.8571587702361505 14.284081206480884 GG663393.1 55852 759839 13.604508343479194 73.44474770453077 GG663392.1 60589 45719 0.7545759131195432 0.8536378408092519 GG663391.1 76172 0 0.0 0.0 GG663390.1 87620 10478 0.11958456973293768 1.2843010833717337 GG663389.1 88906 717 0.008064697545722449 0.09385894898318568 GG663388.1 95026 5257 0.05532170142908257 0.39332889915406377 GG663387.1 113334 182374 1.6091728872183104 6.821823394743606 GG663386.1 144210 75630 0.5244435198668608 1.2115626929981094 GG663385.1 156336 328792 2.1031112475693376 16.888480264938675 GG663384.1 204511 6047999 29.5729765147107 65.54419825591644 GG663383.1 258077 14921125 57.81656249878912 192.72502335313408 GG663382.1 261570 8371134 32.00341782314486 75.08729873800529 GG663381.1 280411 11099599 39.58332233756878 64.69644343004686 GG663380.1 351122 24955044 71.07228826447788 144.0759185920857 GG663379.1 441739 23592441 53.40810071105336 130.6637487706137 GG663378.1 530530 23531792 44.35525229487494 109.19129091389428 GG663377.1 695743 28121728 40.41970670204371 96.46830565636502 GG663376.1 920403 53839286 58.49533954148346 267.3762214961134 GG663375.1 915096 36977604 40.40844239292927 80.18100161228342 GG663374.1 967551 55462420 57.32247705805689 125.2410638540509 GG663373.1 1058542 1035991264 978.6964182809941 1388.1853128252571 GG663372.1 1221551 82237045 67.32182692331307 194.33697132449018 GG663371.1 1250234 65549705 52.42994911352595 172.79622801682578 GG663370.1 1327755 73285133 55.1947708726384 135.44553451004887 GG663369.1 1498222 74795413 49.92278380640519 163.2357931004462 GG663368.1 1769553 84859593 47.95538364773477 112.93264816509303 GG663367.1 2225114 135261964 60.788779361416985 214.9358218312738 GG663366.1 2702831 368885127 136.48101823606433 186.4493154793152 GG663365.1 2818386 337521772 119.7571134684887 489.8290302561302 GG663364.1 2928037 140914094 48.12579007710627 97.5964990807672 GG663363.1 3777229 336608149 89.11510236737037 235.69999140688373 GG663450.1 4245 16552 3.899175500588928 12.378556304172157 GG663449.1 40201 117942 2.933807616725952 7.2586193114989745