BamQC report ----------------------------------- >>>>>>> Input bam file = ../hcapsulatum/2-alignment/pathogen/bam/genome/SRR950197_hisat2.bam outfile = ../hcapsulatum/3-qualimap/genome/SRR950197/genome_results.txt >>>>>>> Reference number of bases = 30,483,324 bp number of contigs = 88 >>>>>>> Globals number of windows = 487 number of reads = 16,826,439 number of mapped reads = 11,356,058 (67.49%) number of mapped paired reads (first in pair) = 5,664,424 number of mapped paired reads (second in pair) = 5,691,634 number of mapped paired reads (both in pair) = 8,801,364 number of mapped paired reads (singletons) = 2,554,694 number of mapped bases = 1,523,805,631 bp number of sequenced bases = 902,714,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,501,783 duplication rate = 44.05% >>>>>>> Insert size mean insert size = 2,239.048 std insert size = 25,325.0989 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 32.3405 >>>>>>> ACTG content number of A's = 224,957,114 bp (24.92%) number of C's = 226,158,511 bp (25.05%) number of T's = 224,650,394 bp (24.89%) number of G's = 226,948,003 bp (25.14%) number of N's = 620,956,672 bp (68.79%) GC percentage = 50.19% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 12,851,299 number of insertions = 161,599 mapped reads with insertion percentage = 1.41% number of deletions = 112,830 mapped reads with deletion percentage = 0.99% homopolymer indels = 66.33% >>>>>>> Coverage mean coverageData = 49.9882X std coverageData = 156.1658X There is a 59.17% of reference with a coverageData >= 1X There is a 53.4% of reference with a coverageData >= 2X There is a 49.73% of reference with a coverageData >= 3X There is a 47.03% of reference with a coverageData >= 4X There is a 44.8% of reference with a coverageData >= 5X There is a 42.89% of reference with a coverageData >= 6X There is a 41.18% of reference with a coverageData >= 7X There is a 39.63% of reference with a coverageData >= 8X There is a 38.2% of reference with a coverageData >= 9X There is a 36.85% of reference with a coverageData >= 10X There is a 35.59% of reference with a coverageData >= 11X There is a 34.4% of reference with a coverageData >= 12X There is a 33.27% of reference with a coverageData >= 13X There is a 32.2% of reference with a coverageData >= 14X There is a 31.18% of reference with a coverageData >= 15X There is a 30.21% of reference with a coverageData >= 16X There is a 29.28% of reference with a coverageData >= 17X There is a 28.38% of reference with a coverageData >= 18X There is a 27.52% of reference with a coverageData >= 19X There is a 26.69% of reference with a coverageData >= 20X There is a 25.88% of reference with a coverageData >= 21X There is a 25.11% of reference with a coverageData >= 22X There is a 24.37% of reference with a coverageData >= 23X There is a 23.67% of reference with a coverageData >= 24X There is a 22.98% of reference with a coverageData >= 25X There is a 22.33% of reference with a coverageData >= 26X There is a 21.71% of reference with a coverageData >= 27X There is a 21.12% of reference with a coverageData >= 28X There is a 20.55% of reference with a coverageData >= 29X There is a 20.01% of reference with a coverageData >= 30X There is a 19.49% of reference with a coverageData >= 31X There is a 18.99% of reference with a coverageData >= 32X There is a 18.5% of reference with a coverageData >= 33X There is a 18.04% of reference with a coverageData >= 34X There is a 17.6% of reference with a coverageData >= 35X There is a 17.17% of reference with a coverageData >= 36X There is a 16.76% of reference with a coverageData >= 37X There is a 16.36% of reference with a coverageData >= 38X There is a 15.98% of reference with a coverageData >= 39X There is a 15.61% of reference with a coverageData >= 40X There is a 15.26% of reference with a coverageData >= 41X There is a 14.92% of reference with a coverageData >= 42X There is a 14.59% of reference with a coverageData >= 43X There is a 14.27% of reference with a coverageData >= 44X There is a 13.95% of reference with a coverageData >= 45X There is a 13.65% of reference with a coverageData >= 46X There is a 13.36% of reference with a coverageData >= 47X There is a 13.08% of reference with a coverageData >= 48X There is a 12.81% of reference with a coverageData >= 49X There is a 12.55% of reference with a coverageData >= 50X There is a 12.29% of reference with a coverageData >= 51X >>>>>>> Coverage per contig GG663448.1 2407 65685 27.289156626506024 37.59837820515408 GG663447.1 5093 3486 0.6844688788533281 0.9947883653623851 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 376 0.04020530367835757 0.33651519295408877 GG663437.1 9532 5645 0.5922156945027277 2.922426101501628 GG663436.1 9723 153735 15.811477938907744 19.95293878875919 GG663435.1 10315 0 0.0 0.0 GG663434.1 11106 35988 3.2404105888708807 7.875371988083396 GG663433.1 11483 0 0.0 0.0 GG663432.1 11832 0 0.0 0.0 GG663431.1 11849 1520 0.12828086758376234 0.6639089087347586 GG663430.1 11959 0 0.0 0.0 GG663429.1 12280 0 0.0 0.0 GG663428.1 12330 479 0.038848337388483374 0.19532069546964098 GG663427.1 12422 0 0.0 0.0 GG663426.1 14805 0 0.0 0.0 GG663425.1 15274 0 0.0 0.0 GG663424.1 15855 0 0.0 0.0 GG663423.1 16334 80 0.004897759275131627 0.06981240025392688 GG663422.1 16757 84023 5.014203019633586 12.097345715028627 GG663421.1 17071 0 0.0 0.0 GG663420.1 17227 0 0.0 0.0 GG663419.1 17524 637 0.03635014836795252 0.3472043582672251 GG663418.1 17580 0 0.0 0.0 GG663417.1 18806 0 0.0 0.0 GG663416.1 20314 240 0.011814512159102097 0.12806535177473008 GG663415.1 20172 75368 3.736268094388261 3.724583383490406 GG663414.1 21124 0 0.0 0.0 GG663413.1 21814 533 0.02443384982121573 0.3024893478121244 GG663412.1 22664 0 0.0 0.0 GG663411.1 23942 0 0.0 0.0 GG663410.1 24438 1369 0.056019314182830016 0.9490737805650518 GG663409.1 30061 0 0.0 0.0 GG663408.1 29608 76 0.0025668738178870575 0.05059925865751497 GG663407.1 31202 1441373 46.19489135311839 81.86632727182443 GG663406.1 31468 0 0.0 0.0 GG663405.1 33416 462 0.013825712233660522 0.17891057354163137 GG663404.1 33436 76 0.002272999162579256 0.047621766424463606 GG663403.1 34148 0 0.0 0.0 GG663402.1 35232 38394 1.0897479564032697 2.3327257404136357 GG663401.1 36230 949456 26.206348330113165 36.76522336643493 GG663400.1 40055 75 0.0018724254150543004 0.04323100089194511 GG663399.1 47125 0 0.0 0.0 GG663398.1 49169 0 0.0 0.0 GG663397.1 50304 418 0.008309478371501273 0.05636755242925194 GG663396.1 51171 78 0.0015243008735416545 0.03901252850545033 GG663395.1 53466 0 0.0 0.0 GG663394.1 53864 131 0.0024320510916382 0.03852158669417223 GG663393.1 55852 1201702 21.51582754422402 122.29960766789077 GG663392.1 60589 40959 0.6760137978841044 0.6796461837459654 GG663391.1 76172 0 0.0 0.0 GG663390.1 87620 0 0.0 0.0 GG663389.1 88906 160 0.0017996535666884126 0.04238413398582443 GG663388.1 95026 75 7.892576768463368E-4 0.028082641420740247 GG663387.1 113334 33268 0.29353944976794255 0.47894600765607054 GG663386.1 144210 910926 6.316663199500728 6.307075048111429 GG663385.1 156336 113414 0.7254503121481937 3.2852650279418825 GG663384.1 204511 3297034 16.121548474165206 39.23761870439641 GG663383.1 258077 8893547 34.4608275824657 86.36058261042052 GG663382.1 261570 7344864 28.079917421722676 55.40397050288993 GG663381.1 280411 8347904 29.77024439126853 44.35163403110447 GG663380.1 351122 19660527 55.99343533017014 157.30544230412116 GG663379.1 441739 18581179 42.063705038495584 106.7720445633662 GG663378.1 530530 24746233 46.64436129907828 105.70942118327831 GG663377.1 695743 28754400 41.32905397539034 93.39631517132293 GG663376.1 920403 39815020 43.25824665934379 102.78915758256221 GG663375.1 915096 33096978 36.167766004878175 86.30795498748024 GG663374.1 967551 72250065 74.67313350924137 157.26909007724112 GG663373.1 1058542 55560532 52.4877916983927 256.9175681549345 GG663372.1 1221551 78473430 64.24081352313576 214.58090126025348 GG663371.1 1250234 45234749 36.18102611191185 103.96760276920425 GG663370.1 1327755 89022619 67.04747411984891 322.28379780177 GG663369.1 1498222 100555610 67.11662891080228 163.80435490956043 GG663368.1 1769553 58036343 32.797177027192745 75.95718597596924 GG663367.1 2225114 103149868 46.3571160848388 121.26958939219575 GG663366.1 2702831 248661376 92.00034186377172 215.55598293722247 GG663365.1 2818386 151691674 53.82217836733506 168.8374063050142 GG663364.1 2928037 128404228 43.853348847709235 103.37585014563736 GG663363.1 3777229 194885442 51.59481778838403 143.271162770465 GG663450.1 4245 9275 2.1849234393404005 7.858863613111483 GG663449.1 40201 172527 4.291609661451208 11.54860592192363