BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716989.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 = 2,782,459 number of mapped reads = 2,504,438 (90.01%) number of supplementary alignments = 8,007 (0.29%) number of secondary alignments = 0 number of mapped bases = 143,105,882 bp number of sequenced bases = 143,063,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,332 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.622 >>>>>>> ACTG content number of A's = 34,870,861 bp (24.37%) number of C's = 28,979,288 bp (20.26%) number of T's = 43,795,562 bp (30.61%) number of G's = 35,416,777 bp (24.76%) number of N's = 1,132 bp (0%) GC percentage = 45.01% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 729,111 number of insertions = 8,778 mapped reads with insertion percentage = 0.35% number of deletions = 26,652 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.3468X There is a 3.92% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13569767 0.05444225954405947 0.4327402947894939 chr2 243199373 11936884 0.04908270877820067 0.5639506683528124 chr3 198022430 9320952 0.04707018290806753 0.25557397055336545 chr4 191154276 8925421 0.04669223826308756 0.29501714870685064 chr5 180915260 8408878 0.04647965019645109 0.24850808205402117 chr6 171115067 8074392 0.04718691428850038 0.30194269109984806 chr7 159138663 7807522 0.049061126019388515 0.4426441898187774 chr8 146364022 6962832 0.0475720187574512 0.31618929361140563 chr9 141213431 5967279 0.04225716320142381 0.29902732823899886 chr10 135534747 6908525 0.050972353237210825 0.4669019214072913 chr11 135006516 6308652 0.04672850012661611 0.3125201541639052 chr12 133851895 6412654 0.04790857835819209 0.25497152329507927 chr13 115169878 4359566 0.037853352592767356 0.22633250502130067 chr14 107349540 4332202 0.04035603692386572 0.24799318838131185 chr15 102531392 4148626 0.04046200796727699 0.2385174647996529 chr16 90354753 3432417 0.03798822846652018 0.2619980750142597 chr17 81195210 4198636 0.05171039030504385 0.2790310059651124 chr18 78077248 3659657 0.046872259124706855 0.45069451212497835 chr19 59128983 3283864 0.055537298857313344 0.39912143797185234 chr20 63025520 3146540 0.04992485583617557 0.26699680314456786 chr21 48129895 1879993 0.03906081656733305 0.2675149166100732 chr22 51304566 1773613 0.03457027586979295 0.21759562838093396 chrMT 16571 12402 0.7484159073079476 1.010046582543783 chrX 155270560 7812995 0.05031858582850477 0.2857187202123624 chrY 59373566 461613 0.007774722508666568 0.2131031677281209