BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716225.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 = 1,301,741 number of mapped reads = 1,164,243 (89.44%) number of supplementary alignments = 4,876 (0.37%) number of secondary alignments = 0 number of mapped bases = 66,391,506 bp number of sequenced bases = 66,372,312 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,337 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4309 >>>>>>> ACTG content number of A's = 16,202,389 bp (24.41%) number of C's = 11,724,626 bp (17.66%) number of T's = 21,769,718 bp (32.8%) number of G's = 16,674,516 bp (25.12%) number of N's = 1,063 bp (0%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 374,904 number of insertions = 3,796 mapped reads with insertion percentage = 0.32% number of deletions = 11,432 mapped reads with deletion percentage = 0.97% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.0214X std coverageData = 0.2144X There is a 1.97% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% 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 5302149 0.021272360240177698 0.3568736501368435 chr2 243199373 5654435 0.023250203856405503 0.2295372567571851 chr3 198022430 4369428 0.02206531856012473 0.15778512766395988 chr4 191154276 4466145 0.023364086294360476 0.17829984991653672 chr5 180915260 4048318 0.022376874123277383 0.16082000714410258 chr6 171115067 3815396 0.022297253344733224 0.1730221955439842 chr7 159138663 3662909 0.02301709044771854 0.24713753775521446 chr8 146364022 3376753 0.023070922442948446 0.24015979751350924 chr9 141213431 2763261 0.01956797579686312 0.21348605498294423 chr10 135534747 3182561 0.02348151356345543 0.22805399085337175 chr11 135006516 3026666 0.02241866607386565 0.20174254422898014 chr12 133851895 2987391 0.02231863060287641 0.16383869534363305 chr13 115169878 2138861 0.018571357694761124 0.1441422281804343 chr14 107349540 2013639 0.018757779493046734 0.1549820316310337 chr15 102531392 1865736 0.018196729446528923 0.14312910423260383 chr16 90354753 1907449 0.02111066586613324 0.1647320442572826 chr17 81195210 1723829 0.0212306735828382 0.16412494185037516 chr18 78077248 1786375 0.02287958458781744 0.35961230212532547 chr19 59128983 1292972 0.021866975117769232 0.27621134611690706 chr20 63025520 1353099 0.021469065229449913 0.1616915369959722 chr21 48129895 878643 0.018255660021697533 0.16049799473500295 chr22 51304566 751182 0.014641620786734654 0.12907387081495933 chrMT 16571 1853 0.1118218574618309 0.34843149651250993 chrX 155270560 3810323 0.024539893460808024 0.19013369513132442 chrY 59373566 212133 0.0035728526058212504 0.09381105569655322