BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524489.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 = 2,227,472 number of mapped reads = 2,039,234 (91.55%) number of supplementary alignments = 7,798 (0.35%) number of secondary alignments = 0 number of mapped bases = 117,152,704 bp number of sequenced bases = 117,120,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,514 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2863 >>>>>>> ACTG content number of A's = 28,105,007 bp (24%) number of C's = 21,748,419 bp (18.57%) number of T's = 37,646,888 bp (32.14%) number of G's = 29,617,166 bp (25.29%) number of N's = 3,462 bp (0%) GC percentage = 43.86% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 557,945 number of insertions = 7,451 mapped reads with insertion percentage = 0.36% number of deletions = 19,011 mapped reads with deletion percentage = 0.93% homopolymer indels = 43.22% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.3284X There is a 3.32% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8374200 0.03359750907100047 0.571484621320612 chr2 243199373 9141783 0.037589665167434456 0.3558869722146124 chr3 198022430 7062000 0.035662626703449704 0.20668394825427333 chr4 191154276 7205620 0.03769531161311819 0.24872830630595977 chr5 180915260 6416212 0.035465289108281964 0.21069672330406083 chr6 171115067 6147650 0.03592699408521401 0.23297160713355503 chr7 159138663 7492191 0.04707964022545546 0.44345895989690687 chr8 146364022 5117706 0.03496560104094434 0.30118756201322083 chr9 141213431 5400247 0.03824173778484286 0.3499476169778267 chr10 135534747 4509071 0.03326874546790573 0.3201633955767407 chr11 135006516 4571862 0.0338640099415646 0.28131038068709846 chr12 133851895 8743322 0.06532086826264208 0.3236827944072103 chr13 115169878 4376805 0.03800303582851759 0.2143366148834846 chr14 107349540 4149022 0.03864964861516873 0.23240173338188888 chr15 102531392 2996834 0.02922845327214518 0.18792050826973555 chr16 90354753 3404308 0.03767713249130347 0.23313500912627672 chr17 81195210 3561215 0.043859914889067965 0.24072498082205057 chr18 78077248 3695054 0.047325617829153 0.5999461663970674 chr19 59128983 2042023 0.03453506041191339 0.4149810715465844 chr20 63025520 3771623 0.05984279066638403 0.2806245740160362 chr21 48129895 1433770 0.029789593349414122 0.2259254520399713 chr22 51304566 1200031 0.02339033527737083 0.16728579238225225 chrMT 16571 13427 0.8102709552833263 1.001439220409203 chrX 155270560 5979549 0.03851051351911142 0.26042989471264855 chrY 59373566 347179 0.005847366486291222 0.1487918806878217