BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716154.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 = 11,460,850 number of mapped reads = 10,500,284 (91.62%) number of supplementary alignments = 47,118 (0.41%) number of secondary alignments = 0 number of mapped bases = 604,664,196 bp number of sequenced bases = 604,514,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,153,434 duplication rate = 8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2383 >>>>>>> ACTG content number of A's = 145,351,190 bp (24.04%) number of C's = 111,596,858 bp (18.46%) number of T's = 194,629,557 bp (32.2%) number of G's = 152,923,227 bp (25.3%) number of N's = 13,517 bp (0%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 2,902,137 number of insertions = 36,733 mapped reads with insertion percentage = 0.35% number of deletions = 87,766 mapped reads with deletion percentage = 0.83% homopolymer indels = 42.34% >>>>>>> Coverage mean coverageData = 0.1953X std coverageData = 1.185X There is a 12.42% of reference with a coverageData >= 1X There is a 3.98% of reference with a coverageData >= 2X There is a 1.51% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 50336893 0.20195292913633303 2.330518506511792 chr2 243199373 49595973 0.20393133579336983 1.3417746577392489 chr3 198022430 39447031 0.1992048628026633 0.666923376961287 chr4 191154276 39234589 0.20525090948004743 0.8337974909626645 chr5 180915260 36144350 0.19978607664162767 0.6803086467626833 chr6 171115067 33541476 0.19601708130120418 0.773861664328095 chr7 159138663 34024255 0.21380256914688292 1.3337428396957884 chr8 146364022 31321914 0.21400009081466756 1.0934939702430728 chr9 141213431 25162289 0.17818623074174864 1.17872510428887 chr10 135534747 28561884 0.21073477194744755 1.1254408119931676 chr11 135006516 28934341 0.21431810743119983 1.1762503146758327 chr12 133851895 27770039 0.20746840379062245 0.707038838925684 chr13 115169878 18965779 0.16467655718103652 0.5944027198061886 chr14 107349540 17175921 0.15999994969703643 0.7084194000551872 chr15 102531392 16893314 0.1647623588295768 0.6141847157371376 chr16 90354753 18510031 0.20485951635549265 0.81514113991731 chr17 81195210 16160342 0.19903073100001836 0.7818336324247386 chr18 78077248 15652353 0.20047265241725734 2.381445404098692 chr19 59128983 12050114 0.20379369623184623 1.5445863815289718 chr20 63025520 12830720 0.20357975626381186 0.7380309946962427 chr21 48129895 7647380 0.15889043597539534 0.7712458976983647 chr22 51304566 7246002 0.14123503159543344 0.5592923960519369 chrMT 16571 92830 5.601955222979905 4.517257932257207 chrX 155270560 35588856 0.2292054334060494 0.9520490802736291 chrY 59373566 1775520 0.029904216970899136 0.5610647806178695