BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053667.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 = 13,912,281 number of mapped reads = 10,214,711 (73.42%) number of supplementary alignments = 298 (0%) number of secondary alignments = 0 number of mapped bases = 483,027,214 bp number of sequenced bases = 482,938,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,556,031 duplication rate = 23.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4002 >>>>>>> ACTG content number of A's = 141,930,336 bp (29.39%) number of C's = 94,373,924 bp (19.54%) number of T's = 142,559,723 bp (29.52%) number of G's = 103,760,396 bp (21.49%) number of N's = 314,400 bp (0.07%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 2,777,132 number of insertions = 19,320 mapped reads with insertion percentage = 0.19% number of deletions = 59,350 mapped reads with deletion percentage = 0.58% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.156X std coverageData = 1.3935X There is a 4.49% of reference with a coverageData >= 1X There is a 2.36% of reference with a coverageData >= 2X There is a 1.62% of reference with a coverageData >= 3X There is a 1.21% of reference with a coverageData >= 4X There is a 0.93% of reference with a coverageData >= 5X There is a 0.73% of reference with a coverageData >= 6X There is a 0.59% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 39314654 0.1577314184505081 1.513512380534738 chr2 243199373 39035811 0.16050950509646256 1.4670064527549496 chr3 198022430 33139420 0.16735184998992286 1.3654684953106346 chr4 191154276 31366118 0.1640879746786308 1.433916333827025 chr5 180915260 30245933 0.1671828733518665 1.3499141865357052 chr6 171115067 29041239 0.16971760295076763 1.5038394732646858 chr7 159138663 26639750 0.16739960923260994 1.4591350493483868 chr8 146364022 24831043 0.1696526418220456 1.4683024435545045 chr9 141213431 19812813 0.14030402674657766 1.2601590364452675 chr10 135534747 22290140 0.16446070467818855 1.4309224486784287 chr11 135006516 21876674 0.16204161582837973 1.4842796260396407 chr12 133851895 22316097 0.1667223090117626 1.360336183692503 chr13 115169878 15888564 0.13795763506843342 1.2379207922827462 chr14 107349540 14930905 0.13908680931469292 1.3420336788520124 chr15 102531392 13818784 0.1347761278809128 1.2141723469703165 chr16 90354753 13672559 0.15132086078526494 1.3097831627736047 chr17 81195210 12748251 0.15700742691594738 1.2962537915859698 chr18 78077248 12811916 0.16409282253390897 1.5404648347706424 chr19 59128983 8678269 0.14676844687147755 1.466057856257154 chr20 63025520 10456514 0.16590920630246286 1.4197982308544919 chr21 48129895 6224803 0.12933340078967553 1.2923613711567108 chr22 51304566 5258074 0.10248744721863547 1.0136554199261194 chrMT 16571 17817 1.075191599782753 2.9343536896972444 chrX 155270560 27411634 0.1765410905969554 1.4762106493977263 chrY 59373566 1199432 0.020201447896863733 0.4463370384908878