BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068151.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 = 6,075,088 number of mapped reads = 5,682,041 (93.53%) number of supplementary alignments = 54,221 (0.89%) number of secondary alignments = 0 number of mapped bases = 368,236,114 bp number of sequenced bases = 368,087,163 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 795,029 duplication rate = 11.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1535 >>>>>>> ACTG content number of A's = 99,216,395 bp (26.95%) number of C's = 67,335,150 bp (18.29%) number of T's = 118,186,310 bp (32.11%) number of G's = 83,306,366 bp (22.63%) number of N's = 42,942 bp (0.01%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 2,119,527 number of insertions = 24,466 mapped reads with insertion percentage = 0.43% number of deletions = 84,298 mapped reads with deletion percentage = 1.47% homopolymer indels = 44.46% >>>>>>> Coverage mean coverageData = 0.119X std coverageData = 1.1624X There is a 7.82% of reference with a coverageData >= 1X There is a 2.42% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 23067210 0.09254624886170294 2.0857967782949087 chr2 243199373 44758778 0.1840415024425248 1.4682922456611558 chr3 198022430 12590239 0.0635798631498462 0.36464716912985207 chr4 191154276 18457790 0.09655965007029191 0.48296186843122507 chr5 180915260 20940077 0.1157452223764872 0.5030093704401246 chr6 171115067 22520456 0.13161001187580987 0.6677489578952808 chr7 159138663 29143847 0.1831349242892659 2.2489886033905937 chr8 146364022 13455438 0.09193132175610752 1.334489282160967 chr9 141213431 11635450 0.08239619926804272 1.0309556124882502 chr10 135534747 14339083 0.10579636084022055 0.8950577041017456 chr11 135006516 19763208 0.1463870677175315 0.8365128698477948 chr12 133851895 24987407 0.1866795161921316 0.6522188757674162 chr13 115169878 14471133 0.12565032846522595 0.5132926904631782 chr14 107349540 11360814 0.1058301134778966 0.5512451270365184 chr15 102531392 11834173 0.11541999741893683 0.5122658650053609 chr16 90354753 8641538 0.09564010428980975 0.6016327711886269 chr17 81195210 9822777 0.12097729656712508 0.5193480092820233 chr18 78077248 5986887 0.07667902178109556 2.2628081117715384 chr19 59128983 5591096 0.09455762159819323 1.5781635832958907 chr20 63025520 6832890 0.10841465488900369 0.5140629886487823 chr21 48129895 7073529 0.14696747208777414 0.6239853977181183 chr22 51304566 2471809 0.0481791230823393 0.29469291519578683 chrMT 16571 187785 11.332146521030717 7.091545069426923 chrX 155270560 26990790 0.17383069913575375 0.7356624286539766 chrY 59373566 1311910 0.022095859965695845 1.1746303180664661