BamQC report ----------------------------------- >>>>>>> Input bam file = ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR949624_hisat2.bam outfile = ../hcapsulatum/3-qualimap/genome/SRR949624/genome_results.txt >>>>>>> Reference number of bases = 30,483,324 bp number of contigs = 88 >>>>>>> Globals number of windows = 487 number of reads = 9,218,978 number of mapped reads = 6,036,342 (65.48%) number of mapped paired reads (first in pair) = 3,052,374 number of mapped paired reads (second in pair) = 2,983,968 number of mapped paired reads (both in pair) = 4,705,357 number of mapped paired reads (singletons) = 1,330,985 number of mapped bases = 672,284,054 bp number of sequenced bases = 468,280,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,164,298 duplication rate = 36.99% >>>>>>> Insert size mean insert size = 2,859.9812 std insert size = 31,094.3812 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 37.7113 >>>>>>> ACTG content number of A's = 116,286,443 bp (24.83%) number of C's = 118,061,403 bp (25.21%) number of T's = 114,970,528 bp (24.55%) number of G's = 118,962,201 bp (25.4%) number of N's = 203,945,725 bp (43.55%) GC percentage = 50.62% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 5,525,396 number of insertions = 71,167 mapped reads with insertion percentage = 1.18% number of deletions = 44,627 mapped reads with deletion percentage = 0.74% homopolymer indels = 63.64% >>>>>>> Coverage mean coverageData = 22.0542X std coverageData = 78.7599X There is a 57.12% of reference with a coverageData >= 1X There is a 50.25% of reference with a coverageData >= 2X There is a 45.73% of reference with a coverageData >= 3X There is a 42.32% of reference with a coverageData >= 4X There is a 39.56% of reference with a coverageData >= 5X There is a 37.23% of reference with a coverageData >= 6X There is a 35.19% of reference with a coverageData >= 7X There is a 33.38% of reference with a coverageData >= 8X There is a 31.76% of reference with a coverageData >= 9X There is a 30.29% of reference with a coverageData >= 10X There is a 28.92% of reference with a coverageData >= 11X There is a 27.66% of reference with a coverageData >= 12X There is a 26.48% of reference with a coverageData >= 13X There is a 25.37% of reference with a coverageData >= 14X There is a 24.32% of reference with a coverageData >= 15X There is a 23.33% of reference with a coverageData >= 16X There is a 22.39% of reference with a coverageData >= 17X There is a 21.5% of reference with a coverageData >= 18X There is a 20.66% of reference with a coverageData >= 19X There is a 19.87% of reference with a coverageData >= 20X There is a 19.11% of reference with a coverageData >= 21X There is a 18.38% of reference with a coverageData >= 22X There is a 17.7% of reference with a coverageData >= 23X There is a 17.04% of reference with a coverageData >= 24X There is a 16.41% of reference with a coverageData >= 25X There is a 15.81% of reference with a coverageData >= 26X There is a 15.24% of reference with a coverageData >= 27X There is a 14.69% of reference with a coverageData >= 28X There is a 14.17% of reference with a coverageData >= 29X There is a 13.66% of reference with a coverageData >= 30X There is a 13.19% of reference with a coverageData >= 31X There is a 12.73% of reference with a coverageData >= 32X There is a 12.29% of reference with a coverageData >= 33X There is a 11.87% of reference with a coverageData >= 34X There is a 11.47% of reference with a coverageData >= 35X There is a 11.09% of reference with a coverageData >= 36X There is a 10.72% of reference with a coverageData >= 37X There is a 10.37% of reference with a coverageData >= 38X There is a 10.03% of reference with a coverageData >= 39X There is a 9.71% of reference with a coverageData >= 40X There is a 9.4% of reference with a coverageData >= 41X There is a 9.1% of reference with a coverageData >= 42X There is a 8.81% of reference with a coverageData >= 43X There is a 8.54% of reference with a coverageData >= 44X There is a 8.27% of reference with a coverageData >= 45X There is a 8.02% of reference with a coverageData >= 46X There is a 7.77% of reference with a coverageData >= 47X There is a 7.54% of reference with a coverageData >= 48X There is a 7.31% of reference with a coverageData >= 49X There is a 7.1% of reference with a coverageData >= 50X There is a 6.89% of reference with a coverageData >= 51X >>>>>>> Coverage per contig GG663448.1 2407 53866 22.378894889904444 31.048698703256786 GG663447.1 5093 5740 1.1270371097584921 1.4995762062934215 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 1093 0.11687339606501283 0.5446198979416152 GG663437.1 9532 2618 0.2746537977339488 1.1372417514421946 GG663436.1 9723 158371 16.288285508587883 18.7998381372558 GG663435.1 10315 0 0.0 0.0 GG663434.1 11106 52336 4.712407707545471 11.592408840437939 GG663433.1 11483 0 0.0 0.0 GG663432.1 11832 0 0.0 0.0 GG663431.1 11849 1468 0.12389231158747574 0.9975597117963461 GG663430.1 11959 0 0.0 0.0 GG663429.1 12280 152 0.012377850162866449 0.15633177124809636 GG663428.1 12330 803 0.0651257096512571 0.19154477071066706 GG663427.1 12422 467 0.03759459024311705 0.4146181051385908 GG663426.1 14805 0 0.0 0.0 GG663425.1 15274 9649 0.6317271179782638 0.7355457660974565 GG663424.1 15855 221 0.013938820561337118 0.15233275347165195 GG663423.1 16334 156 0.009550630586506674 0.12482633991198047 GG663422.1 16757 55761 3.327624276421794 7.168673171338527 GG663421.1 17071 0 0.0 0.0 GG663420.1 17227 0 0.0 0.0 GG663419.1 17524 1437 0.08200182606710797 0.6824388046892295 GG663418.1 17580 310 0.01763367463026166 0.20853974678163517 GG663417.1 18806 0 0.0 0.0 GG663416.1 20314 2484 0.12228020084670671 0.6591041468245473 GG663415.1 20172 18540 0.9190957763236169 0.9156306870678693 GG663414.1 21124 156 0.0073849649687559174 0.08561791437056947 GG663413.1 21814 388 0.017786742458971303 0.193539501027936 GG663412.1 22664 151 0.006662548535121779 0.0813520680876579 GG663411.1 23942 7646 0.3193551081780971 0.3210046724718495 GG663410.1 24438 2926 0.11973156559456584 2.0435321452663318 GG663409.1 30061 29122 0.9687635141878181 1.0095895991557333 GG663408.1 29608 529 0.017866792758713862 0.25987316254863957 GG663407.1 31202 248625 7.968239215434908 13.357331189851134 GG663406.1 31468 154 0.004893860429642812 0.08076127111805752 GG663405.1 33416 622 0.018613837682547284 0.2587019281017959 GG663404.1 33436 192 0.005742313673884436 0.08775994417451022 GG663403.1 34148 78 0.002284174768654094 0.04773842597196035 GG663402.1 35232 51117 1.4508685286103542 3.2221287647505825 GG663401.1 36230 877470 24.21943141043334 33.22200489977381 GG663400.1 40055 1776 0.044339033828485835 0.12749009140297082 GG663399.1 47125 559 0.01186206896551724 0.16607293103119886 GG663398.1 49169 2291 0.04659439890988224 0.8037548936732216 GG663397.1 50304 42005 0.8350230597964376 0.9520697571774119 GG663396.1 51171 145 0.0028336362392761523 0.053156436533496235 GG663395.1 53466 86961 1.6264728986645718 1.6259024894430247 GG663394.1 53864 2616 0.04856676073072924 0.5764042336225302 GG663393.1 55852 140861 2.5220403924658026 14.793532381336162 GG663392.1 60589 22035 0.3636798758850616 0.4316533553270006 GG663391.1 76172 8554 0.11229848238197764 0.1580782526034421 GG663390.1 87620 465 0.00530700753252682 0.08401939439107846 GG663389.1 88906 224 0.0025195149933637776 0.05013149745980059 GG663388.1 95026 60986 0.641782249068676 0.7863799869626344 GG663387.1 113334 3766 0.03322921629872765 0.3309144408705463 GG663386.1 144210 1391771 9.651002010956244 9.628395979846305 GG663385.1 156336 207739 1.3287982294545082 3.0836263231354204 GG663384.1 204511 1870205 9.144764829275687 20.504976094530825 GG663383.1 258077 7891635 30.578606384916128 230.464958507977 GG663382.1 261570 4533199 17.330729823756545 28.256555419938874 GG663381.1 280411 3555103 12.678186661721545 19.922291566792794 GG663380.1 351122 7505343 21.375313993426786 37.97589148260359 GG663379.1 441739 10155686 22.99024084357505 41.50391101659749 GG663378.1 530530 14403960 27.150132885981943 147.59730383360773 GG663377.1 695743 14744948 21.193095726439218 44.06735031793763 GG663376.1 920403 25343498 27.53521881175963 107.01202354229557 GG663375.1 915096 15185750 16.594707003418222 23.707735736802842 GG663374.1 967551 22124640 22.86663958799071 66.0333972336439 GG663373.1 1058542 43745976 41.32663229234173 187.86864330828038 GG663372.1 1221551 33795470 27.666032773089295 62.97482162346303 GG663371.1 1250234 21984345 17.58418424071014 33.80121449411398 GG663370.1 1327755 30630513 23.069401357931245 85.41875905202808 GG663369.1 1498222 31731378 21.179356597353397 42.13531959424761 GG663368.1 1769553 28677334 16.20597631153178 28.330585853236542 GG663367.1 2225114 52148749 23.436439211653873 51.52372031041856 GG663366.1 2702831 96745288 35.79405741609446 151.61042973734786 GG663365.1 2818386 57104639 20.261468443286336 37.245512669685006 GG663364.1 2928037 63796974 21.788308685989964 44.64274124617948 GG663363.1 3777229 80952860 21.431811521091255 50.97851324565329 GG663450.1 4245 2789 0.6570082449941107 2.46996306912117 GG663449.1 40201 96370 2.3972040496505063 8.533925302694081