BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708626.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,148,117 number of mapped reads = 2,328,637 (73.97%) number of supplementary alignments = 779 (0.02%) number of secondary alignments = 0 number of mapped bases = 113,472,563 bp number of sequenced bases = 113,451,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,738 duplication rate = 2.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7568 >>>>>>> ACTG content number of A's = 33,402,480 bp (29.44%) number of C's = 21,384,633 bp (18.85%) number of T's = 35,806,376 bp (31.56%) number of G's = 22,848,525 bp (20.14%) number of N's = 9,750 bp (0.01%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 718,062 number of insertions = 5,288 mapped reads with insertion percentage = 0.23% number of deletions = 13,619 mapped reads with deletion percentage = 0.58% homopolymer indels = 48.22% >>>>>>> Coverage mean coverageData = 0.0367X std coverageData = 0.3785X There is a 3.15% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% 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 8958763 0.03594279109138107 0.7019150312414414 chr2 243199373 9852511 0.04051207401755925 0.37134439018794974 chr3 198022430 7672391 0.03874506034493163 0.22440196947604024 chr4 191154276 7730728 0.04044234929905518 0.23154410456137084 chr5 180915260 7189323 0.039738621274954915 0.2291564141664451 chr6 171115067 6792431 0.03969510762018402 0.28141639141267755 chr7 159138663 6487352 0.040765404696154826 0.5620066444784926 chr8 146364022 5986953 0.04090454005151621 0.6177242949058076 chr9 141213431 4778541 0.033839139564564504 0.3133938840746655 chr10 135534747 5273308 0.038907424971988916 0.29921074166214384 chr11 135006516 5130423 0.038001299137294976 0.3346756023668196 chr12 133851895 5104746 0.03813727104872142 0.2312531681981243 chr13 115169878 3861486 0.03352861066675785 0.2088608050126687 chr14 107349540 3487490 0.03248723748606654 0.2221769609200577 chr15 102531392 3159546 0.030815401394335893 0.19885720039465846 chr16 90354753 2908058 0.03218489236531918 0.22105633946882516 chr17 81195210 2686400 0.03308569557243586 0.2548698242530856 chr18 78077248 3183879 0.040778576109649765 0.6323250449174658 chr19 59128983 1823364 0.030837060059023848 0.5207092899068626 chr20 63025520 2205016 0.03498608182844029 0.22001103748141962 chr21 48129895 1491095 0.03098064103401846 0.21695759808598208 chr22 51304566 1090340 0.021252299454204523 0.16272101776700745 chrMT 16571 2763 0.16673707078631345 0.4846509851007074 chrX 155270560 6361428 0.04096995592725369 0.2660800224615524 chrY 59373566 254228 0.004281838149994225 0.08832764035274342