BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716597.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 = 1,271,269 number of mapped reads = 1,156,533 (90.97%) number of supplementary alignments = 7,754 (0.61%) number of secondary alignments = 0 number of mapped bases = 68,036,230 bp number of sequenced bases = 68,016,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,466 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0486 >>>>>>> ACTG content number of A's = 16,962,815 bp (24.94%) number of C's = 13,808,301 bp (20.3%) number of T's = 20,636,813 bp (30.34%) number of G's = 16,608,045 bp (24.42%) number of N's = 859 bp (0%) GC percentage = 44.72% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 333,811 number of insertions = 5,356 mapped reads with insertion percentage = 0.46% number of deletions = 12,033 mapped reads with deletion percentage = 1.03% homopolymer indels = 39.54% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 0.2027X There is a 1.99% of reference with a coverageData >= 1X There is a 0.15% 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 5545251 0.02224769181217005 0.3118242654171722 chr2 243199373 5845983 0.024037821018559946 0.26044273590839323 chr3 198022430 4511014 0.022780318371004738 0.16368807514548428 chr4 191154276 4317777 0.02258791741598289 0.17337828027389365 chr5 180915260 4050796 0.022390571143639293 0.16175796988268087 chr6 171115067 3968356 0.02319115475669948 0.17609348392291407 chr7 159138663 3687451 0.02317130815658543 0.24543547104834726 chr8 146364022 3426404 0.02341015198393496 0.20556921130167874 chr9 141213431 2785869 0.01972807388271729 0.17224693941284588 chr10 135534747 3268643 0.02411664220688736 0.20648356311708854 chr11 135006516 3141319 0.02326790656533941 0.19501275377770494 chr12 133851895 3103097 0.02318306363910649 0.16623443613626276 chr13 115169878 2136899 0.01855432199033848 0.14738641901737012 chr14 107349540 2048813 0.01908543809316742 0.15260154682169033 chr15 102531392 2010007 0.01960382045725079 0.15231395303934228 chr16 90354753 2059925 0.022798191922454816 0.16923328059502496 chr17 81195210 1945463 0.023960317363548908 0.17654578503084378 chr18 78077248 1746197 0.022364991655443592 0.2676629611035133 chr19 59128983 1402460 0.023718655874734054 0.24776290539830717 chr20 63025520 1406257 0.022312501348660033 0.16416812081832352 chr21 48129895 858211 0.01783114216226734 0.15368796536747217 chr22 51304566 880356 0.017159408384820954 0.1416733452445064 chrMT 16571 5141 0.310240782089192 0.6153181180615347 chrX 155270560 3685110 0.023733475296282825 0.1750740917631917 chrY 59373566 199431 0.0033589190179346817 0.08739895972040719