BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054605.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 4,399,173 number of mapped reads = 3,733,948 (84.88%) number of supplementary alignments = 108 (0%) number of secondary alignments = 0 number of mapped bases = 175,482,558 bp number of sequenced bases = 175,450,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 952,680 duplication rate = 17.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5938 >>>>>>> ACTG content number of A's = 53,440,460 bp (30.46%) number of C's = 35,501,551 bp (20.23%) number of T's = 50,508,735 bp (28.79%) number of G's = 35,981,724 bp (20.51%) number of N's = 17,545 bp (0.01%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 885,354 number of insertions = 6,887 mapped reads with insertion percentage = 0.18% number of deletions = 21,535 mapped reads with deletion percentage = 0.58% homopolymer indels = 43.35% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.602X There is a 2.59% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 16826104 0.06750676861904388 0.7028464214969435 chr2 243199373 13651972 0.05613489801225762 0.6039271950701267 chr3 198022430 13183988 0.06657825580667806 0.6370416886689466 chr4 191154276 10661147 0.055772474584874054 0.5762160340562623 chr5 180915260 8735734 0.04828633029629452 0.5070013847032704 chr6 171115067 8667790 0.05065474450592945 0.5746428835930232 chr7 159138663 12309023 0.07734778442872804 0.7688308191663429 chr8 146364022 7965858 0.05442497337221302 0.56962751837019 chr9 141213431 8278617 0.0586248555918169 0.6099713798480484 chr10 135534747 7723862 0.056988057829923125 0.5959863493347461 chr11 135006516 7932938 0.05875966757041564 0.6005389934276646 chr12 133851895 7222157 0.05395632986742548 0.5501290099244955 chr13 115169878 5335767 0.046329535922578644 0.5240710962796323 chr14 107349540 3484820 0.0324623654651897 0.4310696822918669 chr15 102531392 4898485 0.04777546568371958 0.5321499226059805 chr16 90354753 3992814 0.04419041464260325 0.5236541584968313 chr17 81195210 3057423 0.03765521389747006 0.43273460300545213 chr18 78077248 6868087 0.08796528023118848 0.7794592155593227 chr19 59128983 3254453 0.055039894733180175 0.6030297549142718 chr20 63025520 3330117 0.05283759657992509 0.5432591266554307 chr21 48129895 1957578 0.04067280844888608 0.5361992790148177 chr22 51304566 1676700 0.03268130169934583 0.4046151146026826 chrMT 16571 14300 0.8629533522418683 2.08880765668114 chrX 155270560 14015708 0.0902663582845325 0.7977352477840693 chrY 59373566 437116 0.007362131491310459 0.18280989109881166