BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716910.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,427,915 number of mapped reads = 1,297,908 (90.9%) number of supplementary alignments = 6,048 (0.42%) number of secondary alignments = 0 number of mapped bases = 75,504,952 bp number of sequenced bases = 75,482,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,835 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.341 >>>>>>> ACTG content number of A's = 19,504,322 bp (25.84%) number of C's = 14,795,127 bp (19.6%) number of T's = 22,442,021 bp (29.73%) number of G's = 18,740,099 bp (24.83%) number of N's = 570 bp (0%) GC percentage = 44.43% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 388,446 number of insertions = 5,847 mapped reads with insertion percentage = 0.45% number of deletions = 14,265 mapped reads with deletion percentage = 1.09% homopolymer indels = 40.32% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2084X There is a 2.21% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5895289 0.023652053408524908 0.2710002925288344 chr2 243199373 6238051 0.02564994688534826 0.2653188102540913 chr3 198022430 4985861 0.025178263896670695 0.17224358776747703 chr4 191154276 4803382 0.02512830003342431 0.1860125662109548 chr5 180915260 4456330 0.024632139931147875 0.16923900655731347 chr6 171115067 4323082 0.025264180856733088 0.19147847874184915 chr7 159138663 4098718 0.025755639281699886 0.25768146826965976 chr8 146364022 5347146 0.03653319939513551 0.23950695371167932 chr9 141213431 3148961 0.022299302394260218 0.18215018231761188 chr10 135534747 3634168 0.02681355209966932 0.2658781482877913 chr11 135006516 3326039 0.024636136821722 0.18985397386995276 chr12 133851895 3420850 0.025556978479834 0.17362307113577852 chr13 115169878 2342124 0.02033625493638189 0.15460870807821914 chr14 107349540 2261302 0.021064850394328656 0.16377614132905566 chr15 102531392 2175220 0.02121516110890214 0.15888809886373975 chr16 90354753 2219770 0.024567274286057757 0.18256140632863294 chr17 81195210 2157569 0.026572614320475307 0.18408331380002074 chr18 78077248 1110821 0.014227204831809646 0.24550482040243218 chr19 59128983 1648398 0.027878003584130645 0.24680735179472163 chr20 63025520 1613668 0.025603406366183096 0.17766922835869856 chr21 48129895 988371 0.020535490468034472 0.17013221643868842 chr22 51304566 920949 0.01795062451166627 0.1475913814962139 chrMT 16571 2848 0.17186651378914972 0.4448000589414112 chrX 155270560 4157978 0.0267789206144423 0.1846274907883657 chrY 59373566 228057 0.003841052767489155 0.11685876972609271