BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438279.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 680,728,418 number of mapped reads = 678,760,781 (99.71%) number of supplementary alignments = 10,312,512 (1.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 339,508,334 number of mapped paired reads (second in pair) = 339,252,447 number of mapped paired reads (both in pair) = 677,423,194 number of mapped paired reads (singletons) = 1,337,587 number of mapped bases = 97,506,516,872 bp number of sequenced bases = 97,481,160,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 313,990,348 duplication rate = 43.56% >>>>>>> Insert size mean insert size = 39,104.6688 std insert size = 1,931,722.0928 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 55.1543 >>>>>>> ACTG content number of A's = 29,470,100,758 bp (30.23%) number of C's = 19,484,043,671 bp (19.99%) number of T's = 28,210,325,783 bp (28.94%) number of G's = 20,316,086,235 bp (20.84%) number of N's = 604,398 bp (0%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 498,217,774 number of insertions = 11,835,939 mapped reads with insertion percentage = 1.72% number of deletions = 10,519,382 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.24% >>>>>>> Coverage mean coverageData = 31.4975X std coverageData = 70.0131X There is a 91.24% of reference with a coverageData >= 1X There is a 90.47% of reference with a coverageData >= 2X There is a 89.59% of reference with a coverageData >= 3X There is a 88.64% of reference with a coverageData >= 4X There is a 87.56% of reference with a coverageData >= 5X There is a 86.39% of reference with a coverageData >= 6X There is a 85.11% of reference with a coverageData >= 7X There is a 83.74% of reference with a coverageData >= 8X There is a 82.28% of reference with a coverageData >= 9X There is a 80.74% of reference with a coverageData >= 10X There is a 79.11% of reference with a coverageData >= 11X There is a 77.42% of reference with a coverageData >= 12X There is a 75.67% of reference with a coverageData >= 13X There is a 73.88% of reference with a coverageData >= 14X There is a 72.04% of reference with a coverageData >= 15X There is a 70.17% of reference with a coverageData >= 16X There is a 68.27% of reference with a coverageData >= 17X There is a 66.36% of reference with a coverageData >= 18X There is a 64.44% of reference with a coverageData >= 19X There is a 62.51% of reference with a coverageData >= 20X There is a 60.59% of reference with a coverageData >= 21X There is a 58.68% of reference with a coverageData >= 22X There is a 56.78% of reference with a coverageData >= 23X There is a 54.91% of reference with a coverageData >= 24X There is a 53.05% of reference with a coverageData >= 25X There is a 51.22% of reference with a coverageData >= 26X There is a 49.43% of reference with a coverageData >= 27X There is a 47.66% of reference with a coverageData >= 28X There is a 45.94% of reference with a coverageData >= 29X There is a 44.25% of reference with a coverageData >= 30X There is a 42.6% of reference with a coverageData >= 31X There is a 40.99% of reference with a coverageData >= 32X There is a 39.42% of reference with a coverageData >= 33X There is a 37.9% of reference with a coverageData >= 34X There is a 36.42% of reference with a coverageData >= 35X There is a 34.99% of reference with a coverageData >= 36X There is a 33.6% of reference with a coverageData >= 37X There is a 32.25% of reference with a coverageData >= 38X There is a 30.95% of reference with a coverageData >= 39X There is a 29.69% of reference with a coverageData >= 40X There is a 28.47% of reference with a coverageData >= 41X There is a 27.3% of reference with a coverageData >= 42X There is a 26.17% of reference with a coverageData >= 43X There is a 25.07% of reference with a coverageData >= 44X There is a 24.02% of reference with a coverageData >= 45X There is a 23.01% of reference with a coverageData >= 46X There is a 22.04% of reference with a coverageData >= 47X There is a 21.1% of reference with a coverageData >= 48X There is a 20.2% of reference with a coverageData >= 49X There is a 19.34% of reference with a coverageData >= 50X There is a 18.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7950122486 31.896099011123425 30.416512647310693 chr2 243199373 8625370840 35.46625442985825 126.4127860471399 chr3 198022430 7121749558 35.964357966923245 79.69140828697782 chr4 191154276 6607779322 34.567781899893255 25.800588469927238 chr5 180915260 6365567073 35.1853518216208 28.08559904984219 chr6 171115067 5758242711 33.65128981307064 26.120758810804364 chr7 159138663 5237631626 32.912376711371515 26.185442005940082 chr8 146364022 5040541397 34.43839085673664 26.378011968860672 chr9 141213431 4240202821 30.02690884976798 30.951003972806866 chr10 135534747 4713178464 34.77468743863889 33.06355528746187 chr11 135006516 4663473889 34.54258377425279 27.18454459475146 chr12 133851895 4618397921 34.503791829021175 26.113424393612476 chr13 115169878 3383539405 29.378683591207764 26.31728356807806 chr14 107349540 3159362102 29.430606800923414 28.551314644793106 chr15 102531392 2850673372 27.80293251065976 28.352655051213 chr16 90354753 2617071377 28.96440187269396 49.86808405075923 chr17 81195210 2376407173 29.267824702959693 35.541678208458116 chr18 78077248 2700238523 34.58419183780658 27.231661539932716 chr19 59128983 1437278043 24.307504883011433 117.24051341921081 chr20 63025520 2127453411 33.75542813450805 29.70213508869599 chr21 48129895 1214404340 25.23180946062733 50.891975893591656 chr22 51304566 1052287606 20.510603403213665 27.49460946056158 chrMT 16571 314925068 19004.59042906282 7377.554622392168 chrX 155270560 2833711192 18.25015116838633 19.908667504017426 chrY 59373566 496907152 8.3691646885417 26.070547890107377