BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438301.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 = 1,417,839,826 number of mapped reads = 1,412,113,161 (99.6%) number of supplementary alignments = 24,718,770 (1.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 706,548,696 number of mapped paired reads (second in pair) = 705,564,465 number of mapped paired reads (both in pair) = 1,409,299,908 number of mapped paired reads (singletons) = 2,813,253 number of mapped bases = 154,373,676,711 bp number of sequenced bases = 154,337,911,741 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 784,053,474 duplication rate = 50.39% >>>>>>> Insert size mean insert size = 180,023.8577 std insert size = 4,304,229.5636 median insert size = 120 >>>>>>> Mapping quality mean mapping quality = 52.6821 >>>>>>> ACTG content number of A's = 46,880,140,715 bp (30.38%) number of C's = 30,543,250,937 bp (19.79%) number of T's = 45,716,900,203 bp (29.62%) number of G's = 31,197,187,801 bp (20.21%) number of N's = 432,085 bp (0%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 512,875,408 number of insertions = 22,497,679 mapped reads with insertion percentage = 1.58% number of deletions = 15,484,065 mapped reads with deletion percentage = 1.09% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 49.8672X std coverageData = 565.4532X There is a 83.68% of reference with a coverageData >= 1X There is a 80.58% of reference with a coverageData >= 2X There is a 75.91% of reference with a coverageData >= 3X There is a 72.76% of reference with a coverageData >= 4X There is a 69.44% of reference with a coverageData >= 5X There is a 66.77% of reference with a coverageData >= 6X There is a 64.23% of reference with a coverageData >= 7X There is a 62.04% of reference with a coverageData >= 8X There is a 60% of reference with a coverageData >= 9X There is a 58.18% of reference with a coverageData >= 10X There is a 56.5% of reference with a coverageData >= 11X There is a 54.96% of reference with a coverageData >= 12X There is a 53.52% of reference with a coverageData >= 13X There is a 52.18% of reference with a coverageData >= 14X There is a 50.92% of reference with a coverageData >= 15X There is a 49.74% of reference with a coverageData >= 16X There is a 48.63% of reference with a coverageData >= 17X There is a 47.57% of reference with a coverageData >= 18X There is a 46.56% of reference with a coverageData >= 19X There is a 45.6% of reference with a coverageData >= 20X There is a 44.67% of reference with a coverageData >= 21X There is a 43.79% of reference with a coverageData >= 22X There is a 42.94% of reference with a coverageData >= 23X There is a 42.12% of reference with a coverageData >= 24X There is a 41.33% of reference with a coverageData >= 25X There is a 40.57% of reference with a coverageData >= 26X There is a 39.84% of reference with a coverageData >= 27X There is a 39.12% of reference with a coverageData >= 28X There is a 38.43% of reference with a coverageData >= 29X There is a 37.76% of reference with a coverageData >= 30X There is a 37.11% of reference with a coverageData >= 31X There is a 36.48% of reference with a coverageData >= 32X There is a 35.87% of reference with a coverageData >= 33X There is a 35.27% of reference with a coverageData >= 34X There is a 34.69% of reference with a coverageData >= 35X There is a 34.12% of reference with a coverageData >= 36X There is a 33.57% of reference with a coverageData >= 37X There is a 33.03% of reference with a coverageData >= 38X There is a 32.5% of reference with a coverageData >= 39X There is a 31.99% of reference with a coverageData >= 40X There is a 31.49% of reference with a coverageData >= 41X There is a 31% of reference with a coverageData >= 42X There is a 30.52% of reference with a coverageData >= 43X There is a 30.05% of reference with a coverageData >= 44X There is a 29.6% of reference with a coverageData >= 45X There is a 29.15% of reference with a coverageData >= 46X There is a 28.71% of reference with a coverageData >= 47X There is a 28.28% of reference with a coverageData >= 48X There is a 27.87% of reference with a coverageData >= 49X There is a 27.46% of reference with a coverageData >= 50X There is a 27.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11681569307 46.86676109424818 92.86892632930085 chr2 243199373 15093778136 62.06339247428899 1990.9251924310568 chr3 198022430 10706512673 54.067171446184155 91.72004982039147 chr4 191154276 11972392758 62.63209491583646 103.39673014548917 chr5 180915260 10078276793 55.707168057575686 98.08289472662236 chr6 171115067 11865327074 69.34121747443783 117.88019145329919 chr7 159138663 8383876774 52.68284033528672 95.41529609887871 chr8 146364022 7530176688 51.448276599012836 88.69895238583928 chr9 141213431 5322076003 37.68817148136568 79.63699449724095 chr10 135534747 6563186432 48.42438250908455 86.12896037957312 chr11 135006516 7561590581 56.00907870994908 103.92799126295101 chr12 133851895 6710995927 50.137474161273545 105.80917482688308 chr13 115169878 4808962826 41.75538699450563 85.93915860438064 chr14 107349540 4943916104 46.05437623673096 94.39827769342371 chr15 102531392 4480558306 43.69938043950481 96.87801797141667 chr16 90354753 2548146933 28.20158152609858 64.73321257278762 chr17 81195210 3124474144 38.48101561656162 77.36566318141705 chr18 78077248 4489239384 57.49740800290502 92.35481230545025 chr19 59128983 1331217224 22.513785227795985 52.630754112794605 chr20 63025520 2042283379 32.404070271851786 64.94609712103127 chr21 48129895 1514013918 31.45682985595543 74.74402895022993 chr22 51304566 831533586 16.207789107893436 47.741034953407805 chrMT 16571 448326 27.054854866936214 20.89189218329793 chrX 155270560 10666421335 68.6957098306337 131.5382946560862 chrY 59373566 122702100 2.066611596143644 13.532126381074892