BamQC report ----------------------------------- >>>>>>> Input bam file = ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949601_hisat2.bam outfile = ../hcapsulatum/3-qualimap/genome/SRR949601/genome_results.txt >>>>>>> Reference number of bases = 30,483,324 bp number of contigs = 88 >>>>>>> Globals number of windows = 487 number of reads = 11,190,319 number of mapped reads = 7,433,632 (66.43%) number of mapped paired reads (first in pair) = 3,758,614 number of mapped paired reads (second in pair) = 3,675,018 number of mapped paired reads (both in pair) = 5,828,135 number of mapped paired reads (singletons) = 1,605,497 number of mapped bases = 868,539,584 bp number of sequenced bases = 576,788,009 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,171,621 duplication rate = 39.52% >>>>>>> Insert size mean insert size = 2,964.732 std insert size = 32,142.157 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 36.6273 >>>>>>> ACTG content number of A's = 143,447,519 bp (24.87%) number of C's = 144,414,773 bp (25.04%) number of T's = 142,092,544 bp (24.64%) number of G's = 146,833,173 bp (25.46%) number of N's = 291,685,073 bp (50.57%) GC percentage = 50.49% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 6,625,990 number of insertions = 81,514 mapped reads with insertion percentage = 1.1% number of deletions = 51,694 mapped reads with deletion percentage = 0.7% homopolymer indels = 62.69% >>>>>>> Coverage mean coverageData = 28.4923X std coverageData = 102.6435X There is a 58.99% of reference with a coverageData >= 1X There is a 52.8% of reference with a coverageData >= 2X There is a 48.64% of reference with a coverageData >= 3X There is a 45.46% of reference with a coverageData >= 4X There is a 42.88% of reference with a coverageData >= 5X There is a 40.65% of reference with a coverageData >= 6X There is a 38.7% of reference with a coverageData >= 7X There is a 36.94% of reference with a coverageData >= 8X There is a 35.35% of reference with a coverageData >= 9X There is a 33.88% of reference with a coverageData >= 10X There is a 32.54% of reference with a coverageData >= 11X There is a 31.28% of reference with a coverageData >= 12X There is a 30.11% of reference with a coverageData >= 13X There is a 29% of reference with a coverageData >= 14X There is a 27.95% of reference with a coverageData >= 15X There is a 26.97% of reference with a coverageData >= 16X There is a 26.03% of reference with a coverageData >= 17X There is a 25.13% of reference with a coverageData >= 18X There is a 24.27% of reference with a coverageData >= 19X There is a 23.45% of reference with a coverageData >= 20X There is a 22.66% of reference with a coverageData >= 21X There is a 21.9% of reference with a coverageData >= 22X There is a 21.17% of reference with a coverageData >= 23X There is a 20.47% of reference with a coverageData >= 24X There is a 19.8% of reference with a coverageData >= 25X There is a 19.15% of reference with a coverageData >= 26X There is a 18.53% of reference with a coverageData >= 27X There is a 17.94% of reference with a coverageData >= 28X There is a 17.36% of reference with a coverageData >= 29X There is a 16.81% of reference with a coverageData >= 30X There is a 16.28% of reference with a coverageData >= 31X There is a 15.77% of reference with a coverageData >= 32X There is a 15.28% of reference with a coverageData >= 33X There is a 14.81% of reference with a coverageData >= 34X There is a 14.35% of reference with a coverageData >= 35X There is a 13.92% of reference with a coverageData >= 36X There is a 13.5% of reference with a coverageData >= 37X There is a 13.09% of reference with a coverageData >= 38X There is a 12.7% of reference with a coverageData >= 39X There is a 12.32% of reference with a coverageData >= 40X There is a 11.96% of reference with a coverageData >= 41X There is a 11.61% of reference with a coverageData >= 42X There is a 11.27% of reference with a coverageData >= 43X There is a 10.95% of reference with a coverageData >= 44X There is a 10.64% of reference with a coverageData >= 45X There is a 10.34% of reference with a coverageData >= 46X There is a 10.04% of reference with a coverageData >= 47X There is a 9.76% of reference with a coverageData >= 48X There is a 9.49% of reference with a coverageData >= 49X There is a 9.23% of reference with a coverageData >= 50X There is a 8.97% of reference with a coverageData >= 51X >>>>>>> Coverage per contig GG663448.1 2407 55122 22.90070627336934 30.001745702762864 GG663447.1 5093 10138 1.990575299430591 2.9399087937318424 GG663446.1 5267 0 0.0 0.0 GG663445.1 5726 0 0.0 0.0 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 1535 0.16413601368691189 0.7509357919471122 GG663437.1 9532 2859 0.29993705413344524 1.1323588798937563 GG663436.1 9723 202598 20.836984469813842 24.273829900805637 GG663435.1 10315 0 0.0 0.0 GG663434.1 11106 66721 6.007653520619485 14.500746737961443 GG663433.1 11483 0 0.0 0.0 GG663432.1 11832 0 0.0 0.0 GG663431.1 11849 3248 0.2741159591526711 1.5843520827293485 GG663430.1 11959 0 0.0 0.0 GG663429.1 12280 300 0.024429967426710098 0.24658432261059893 GG663428.1 12330 550 0.04460665044606651 0.22816999983332759 GG663427.1 12422 999 0.08042183223313476 0.6221875660305252 GG663426.1 14805 0 0.0 0.0 GG663425.1 15274 9432 0.6175199685740475 0.7692769189078376 GG663424.1 15855 148 0.009334594765058341 0.09616371511973987 GG663423.1 16334 0 0.0 0.0 GG663422.1 16757 73262 4.37202363191502 8.41295119547404 GG663421.1 17071 0 0.0 0.0 GG663420.1 17227 0 0.0 0.0 GG663419.1 17524 2195 0.12525679068705775 0.7519682538742776 GG663418.1 17580 4766 0.27110352673492605 0.3221058157877679 GG663417.1 18806 0 0.0 0.0 GG663416.1 20314 2218 0.10918578320370188 0.988957091794663 GG663415.1 20172 389 0.01928415625619671 0.1629313420119425 GG663414.1 21124 78 0.0036924824843779587 0.06065350820422938 GG663413.1 21814 541 0.024800586779132668 0.17415039971143342 GG663412.1 22664 136 0.006000705965407695 0.0582468256417876 GG663411.1 23942 0 0.0 0.0 GG663410.1 24438 5561 0.22755544643587855 3.819895518778351 GG663409.1 30061 466 0.015501812980273444 0.25185358915440176 GG663408.1 29608 617 0.020838962442583087 0.2590005289296644 GG663407.1 31202 357202 11.448048202038331 17.73608765233317 GG663406.1 31468 71 0.0022562603279522053 0.04744649214941727 GG663405.1 33416 778 0.023282259995211874 0.3483040755484831 GG663404.1 33436 78 0.0023328149300155523 0.04824285340356485 GG663403.1 34148 77 0.002254890476748272 0.04743211934634739 GG663402.1 35232 97965 2.780568801089918 6.023081552961735 GG663401.1 36230 1032476 28.497819486613302 39.61359659125 GG663400.1 40055 152 0.003794782174510049 0.06148480952851744 GG663399.1 47125 597 0.0126684350132626 0.1771439439953562 GG663398.1 49169 1527 0.03105615326730257 0.46029650467436434 GG663397.1 50304 145024 2.8829516539440205 2.922888603263056 GG663396.1 51171 509 0.009947040315803873 0.1078399482572666 GG663395.1 53466 173997 3.2543485579620692 3.251792272760165 GG663394.1 53864 24467 0.4542365958710827 0.6510617510010525 GG663393.1 55852 163440 2.926305235264628 17.33341026296976 GG663392.1 60589 51004 0.8418029675353612 0.8994888116274674 GG663391.1 76172 831 0.010909520558735493 0.23284873677455 GG663390.1 87620 232 0.002647797306551016 0.08792581270269993 GG663389.1 88906 78 8.773311137606011E-4 0.029606779694479245 GG663388.1 95026 44080 0.46387304527182033 0.5987904148078584 GG663387.1 113334 4149 0.036608608184657734 0.3220847768227135 GG663386.1 144210 1847041 12.807995284654323 12.78453734848937 GG663385.1 156336 319604 2.044340395046566 4.421742102063194 GG663384.1 204511 2739638 13.396042266675142 23.348472772696212 GG663383.1 258077 8138542 31.53532472866625 151.43286625821654 GG663382.1 261570 5516883 21.09142103452231 36.21521279775536 GG663381.1 280411 4422477 15.771410536676521 24.22309782559654 GG663380.1 351122 9482771 27.007054528055775 42.14874953710861 GG663379.1 441739 11608513 26.27912183438637 45.98983497409104 GG663378.1 530530 15778547 29.74110229393248 166.5807120477755 GG663377.1 695743 17864979 25.677554786753156 50.36032573017886 GG663376.1 920403 27310509 29.672338095377786 107.45269930563437 GG663375.1 915096 16054734 17.544316661858428 27.08731107258234 GG663374.1 967551 24064314 24.871364920298774 77.88225548348744 GG663373.1 1058542 82406196 77.84877312378725 360.8731948084349 GG663372.1 1221551 54345775 44.48915763648018 77.08414082821912 GG663371.1 1250234 27232788 21.782152780999397 49.80297397666817 GG663370.1 1327755 38105329 28.699066469341105 109.83920390672553 GG663369.1 1498222 39233117 26.18645100659315 50.369093236254294 GG663368.1 1769553 35095745 19.83311322124853 33.4571876567509 GG663367.1 2225114 70276557 31.583351235037846 61.56379310594635 GG663366.1 2702831 121713538 45.03187139706478 165.35075082633574 GG663365.1 2818386 76005305 26.96767050361448 48.53444751794978 GG663364.1 2928037 75394656 25.749215600759143 47.854703726567145 GG663363.1 3777229 100932171 26.721221032667067 58.82787135473457 GG663450.1 4245 2250 0.5300353356890459 1.970302516360542 GG663449.1 40201 104992 2.611676326459541 8.29119388913059