BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068951.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,473,671 number of mapped reads = 2,015,461 (81.48%) number of supplementary alignments = 9,334 (0.38%) number of secondary alignments = 0 number of mapped bases = 129,680,238 bp number of sequenced bases = 129,622,687 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,003 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4277 >>>>>>> ACTG content number of A's = 34,848,392 bp (26.88%) number of C's = 21,964,303 bp (16.94%) number of T's = 43,966,273 bp (33.92%) number of G's = 28,537,395 bp (22.02%) number of N's = 306,324 bp (0.24%) GC percentage = 38.96% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 1,367,758 number of insertions = 11,497 mapped reads with insertion percentage = 0.57% number of deletions = 35,558 mapped reads with deletion percentage = 1.74% homopolymer indels = 48.73% >>>>>>> Coverage mean coverageData = 0.0419X std coverageData = 0.3551X There is a 3.56% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11198521 0.044928758672982405 0.5909826755531857 chr2 243199373 11155845 0.04587119145245494 0.3553356299421683 chr3 198022430 8685567 0.04386153124168812 0.23856724614801653 chr4 191154276 8924866 0.04668933484909331 0.2650744212711007 chr5 180915260 8075372 0.04463621255608841 0.2414150503995301 chr6 171115067 7756890 0.04533142601638931 0.28598499689630563 chr7 159138663 7284714 0.04577589042582317 0.4776015495024374 chr8 146364022 7161704 0.048930767972473456 0.58629954844577 chr9 141213431 5495355 0.03891524312584686 0.3482564400545483 chr10 135534747 6033938 0.044519491374414855 0.3633256799181558 chr11 135006516 5817162 0.04308800917431274 0.29700513212128177 chr12 133851895 6016653 0.04495007709827343 0.24556257861653444 chr13 115169878 4101837 0.035615536555487194 0.21416922088101484 chr14 107349540 3729732 0.03474380980114121 0.22402761753709347 chr15 102531392 3607370 0.03518307836881801 0.21438186675114143 chr16 90354753 3147767 0.03483786846276919 0.23636484962626117 chr17 81195210 2913479 0.03588239995930794 0.23019481933189928 chr18 78077248 3454493 0.04424455380394555 0.5667090446623382 chr19 59128983 2015567 0.03408763177949467 0.39660726512838346 chr20 63025520 2429186 0.038542895005070965 0.23090644066676608 chr21 48129895 1763976 0.03665031889223943 0.2385949794152438 chr22 51304566 1236477 0.024100720392021248 0.17362675544345432 chrMT 16571 146849 8.861806770864764 6.064088057412766 chrX 155270560 7181911 0.04625417078421048 0.27429534923264937 chrY 59373566 345007 0.005810784550148125 0.14098085463775173