BamQC report ----------------------------------- >>>>>>> Input bam file = ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949060_hisat2.bam outfile = ../hcapsulatum/3-qualimap/genome/SRR949060/genome_results.txt >>>>>>> Reference number of bases = 30,483,324 bp number of contigs = 88 >>>>>>> Globals number of windows = 487 number of reads = 9,576,101 number of mapped reads = 9,226,209 (96.35%) number of mapped paired reads (first in pair) = 4,633,216 number of mapped paired reads (second in pair) = 4,592,993 number of mapped paired reads (both in pair) = 8,987,885 number of mapped paired reads (singletons) = 238,324 number of mapped bases = 969,956,852 bp number of sequenced bases = 718,189,766 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,837,797 duplication rate = 36.98% >>>>>>> Insert size mean insert size = 2,945.6068 std insert size = 32,376.0387 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 40.5535 >>>>>>> ACTG content number of A's = 181,426,059 bp (25.26%) number of C's = 177,218,602 bp (24.68%) number of T's = 181,033,991 bp (25.21%) number of G's = 178,511,114 bp (24.86%) number of N's = 251,744,425 bp (35.05%) GC percentage = 49.53% >>>>>>> Mismatches and indels general error rate = 0.0008 number of mismatches = 789,163 number of insertions = 26,950 mapped reads with insertion percentage = 0.29% number of deletions = 18,383 mapped reads with deletion percentage = 0.2% homopolymer indels = 82.67% >>>>>>> Coverage mean coverageData = 31.8193X std coverageData = 88.5775X There is a 75.65% of reference with a coverageData >= 1X There is a 68.66% of reference with a coverageData >= 2X There is a 63.57% of reference with a coverageData >= 3X There is a 59.58% of reference with a coverageData >= 4X There is a 56.25% of reference with a coverageData >= 5X There is a 53.4% of reference with a coverageData >= 6X There is a 50.9% of reference with a coverageData >= 7X There is a 48.64% of reference with a coverageData >= 8X There is a 46.57% of reference with a coverageData >= 9X There is a 44.68% of reference with a coverageData >= 10X There is a 42.9% of reference with a coverageData >= 11X There is a 41.22% of reference with a coverageData >= 12X There is a 39.63% of reference with a coverageData >= 13X There is a 38.1% of reference with a coverageData >= 14X There is a 36.64% of reference with a coverageData >= 15X There is a 35.25% of reference with a coverageData >= 16X There is a 33.92% of reference with a coverageData >= 17X There is a 32.65% of reference with a coverageData >= 18X There is a 31.42% of reference with a coverageData >= 19X There is a 30.25% of reference with a coverageData >= 20X There is a 29.13% of reference with a coverageData >= 21X There is a 28.05% of reference with a coverageData >= 22X There is a 27.02% of reference with a coverageData >= 23X There is a 26.04% of reference with a coverageData >= 24X There is a 25.09% of reference with a coverageData >= 25X There is a 24.19% of reference with a coverageData >= 26X There is a 23.32% of reference with a coverageData >= 27X There is a 22.49% of reference with a coverageData >= 28X There is a 21.69% of reference with a coverageData >= 29X There is a 20.92% of reference with a coverageData >= 30X There is a 20.19% of reference with a coverageData >= 31X There is a 19.47% of reference with a coverageData >= 32X There is a 18.8% of reference with a coverageData >= 33X There is a 18.15% of reference with a coverageData >= 34X There is a 17.52% of reference with a coverageData >= 35X There is a 16.93% of reference with a coverageData >= 36X There is a 16.36% of reference with a coverageData >= 37X There is a 15.83% of reference with a coverageData >= 38X There is a 15.31% of reference with a coverageData >= 39X There is a 14.81% of reference with a coverageData >= 40X There is a 14.34% of reference with a coverageData >= 41X There is a 13.88% of reference with a coverageData >= 42X There is a 13.45% of reference with a coverageData >= 43X There is a 13.04% of reference with a coverageData >= 44X There is a 12.65% of reference with a coverageData >= 45X There is a 12.27% of reference with a coverageData >= 46X There is a 11.91% of reference with a coverageData >= 47X There is a 11.57% of reference with a coverageData >= 48X There is a 11.24% of reference with a coverageData >= 49X There is a 10.93% of reference with a coverageData >= 50X There is a 10.63% of reference with a coverageData >= 51X >>>>>>> Coverage per contig GG663448.1 2407 61845 25.693809721645202 29.856121292453626 GG663447.1 5093 1247 0.24484586687610446 0.8666970602398801 GG663446.1 5267 2255 0.42813745965445227 1.7031198005310515 GG663445.1 5726 3108 0.5427872860635696 2.045629381388458 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 11315 1.209901625320787 4.57052888691606 GG663437.1 9532 87070 9.13449433487201 8.107547320919481 GG663436.1 9723 846317 87.04278514861669 101.33773721205068 GG663435.1 10315 0 0.0 0.0 GG663434.1 11106 123829 11.149738879884747 23.282073820176088 GG663433.1 11483 0 0.0 0.0 GG663432.1 11832 0 0.0 0.0 GG663431.1 11849 1209 0.1020339269136636 0.6143254036329295 GG663430.1 11959 0 0.0 0.0 GG663429.1 12280 0 0.0 0.0 GG663428.1 12330 162698 13.19529602595296 29.629785988723384 GG663427.1 12422 1351 0.10875865400096603 0.460635519080461 GG663426.1 14805 0 0.0 0.0 GG663425.1 15274 3095 0.202631923530182 0.9117257251366536 GG663424.1 15855 0 0.0 0.0 GG663423.1 16334 95588 5.8520876698910245 15.163324211543646 GG663422.1 16757 221674 13.228740227964433 19.23896230391788 GG663421.1 17071 0 0.0 0.0 GG663420.1 17227 1155 0.06704591629418935 0.3962296186028236 GG663419.1 17524 13763 0.7853800502168454 2.7273020248331497 GG663418.1 17580 156 0.008873720136518772 0.09378153990768925 GG663417.1 18806 0 0.0 0.0 GG663416.1 20314 3336 0.16422171901151916 1.2899165963380719 GG663415.1 20172 6244 0.30953797342851475 1.0738202780924353 GG663414.1 21124 312 0.014769929937511835 0.12063075522914059 GG663413.1 21814 27053 1.2401668653158522 4.194220662456275 GG663412.1 22664 156 0.006883162725026474 0.08267880499818124 GG663411.1 23942 0 0.0 0.0 GG663410.1 24438 0 0.0 0.0 GG663409.1 30061 78 0.0025947240610758125 0.050872305512161396 GG663408.1 29608 0 0.0 0.0 GG663407.1 31202 1039744 33.32299211589001 43.479233592633065 GG663406.1 31468 0 0.0 0.0 GG663405.1 33416 0 0.0 0.0 GG663404.1 33436 0 0.0 0.0 GG663403.1 34148 1295 0.037923158018039124 0.45901348985916085 GG663402.1 35232 182346 5.175579019073569 9.426696176558456 GG663401.1 36230 1130078 31.19177477228816 39.38849611260457 GG663400.1 40055 0 0.0 0.0 GG663399.1 47125 1246 0.02644031830238727 0.2015881434871447 GG663398.1 49169 156 0.00317273078565763 0.05623757253846729 GG663397.1 50304 7633 0.15173743638676845 0.7887659284870723 GG663396.1 51171 35242 0.688710402376346 1.1143101536184037 GG663395.1 53466 49168 0.9196124639958104 2.006855145211069 GG663394.1 53864 76303 1.4165862171394623 6.544689709631516 GG663393.1 55852 335158 6.000823605242426 34.10994301395943 GG663392.1 60589 35140 0.5799732624733862 0.8070710333404906 GG663391.1 76172 2649 0.03477655831539148 0.3371465241002928 GG663390.1 87620 19748 0.22538233280073042 2.13541641860695 GG663389.1 88906 0 0.0 0.0 GG663388.1 95026 27441 0.2887735988045377 0.7839183939819563 GG663387.1 113334 305605 2.6964988441244464 12.986157549069851 GG663386.1 144210 32941 0.22842382636432979 1.1067390189677626 GG663385.1 156336 92400 0.5910346945041449 3.524510458848075 GG663384.1 204511 3525412 17.23825124320941 27.800917009644028 GG663383.1 258077 6713455 26.01337972775567 60.37982917160991 GG663382.1 261570 5167583 19.75602324425584 28.515076770875577 GG663381.1 280411 5246626 18.710485679948363 26.350502512204557 GG663380.1 351122 14022722 39.93689372924511 69.3984082964675 GG663379.1 441739 16487105 37.32318178834108 101.85086627205362 GG663378.1 530530 16089361 30.326957947712664 57.21447721723668 GG663377.1 695743 19127644 27.49239877368511 43.1251587245898 GG663376.1 920403 24338078 26.442849490929518 53.386294348999975 GG663375.1 915096 22681932 24.786396181384248 44.0251992579815 GG663374.1 967551 23859972 24.660169851511704 44.42565971841708 GG663373.1 1058542 57867280 54.66696645007945 225.66933647751713 GG663372.1 1221551 47571108 38.94320253513771 107.74102715449514 GG663371.1 1250234 30690217 24.547578293343488 39.99361859003767 GG663370.1 1327755 46141021 34.75115589849031 211.49431220920462 GG663369.1 1498222 43997082 29.366196731859496 56.526790375798825 GG663368.1 1769553 46800953 26.447895598492952 46.60533916633125 GG663367.1 2225114 78295840 35.1873387161287 91.8855554531108 GG663366.1 2702831 163103242 60.34533494695007 75.898808053882 GG663365.1 2818386 93211225 33.072554646524644 92.63270843569747 GG663364.1 2928037 83342152 28.463490044695472 46.22156118217069 GG663363.1 3777229 116530905 30.850897575974344 69.92061222608906 GG663450.1 4245 8239 1.940871613663133 6.344639813572125 GG663449.1 40201 88551 2.2027064003383 6.3342023024724154