BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083765.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,228,777 number of mapped reads = 2,005,738 (62.12%) number of supplementary alignments = 12,678 (0.39%) number of secondary alignments = 0 number of mapped bases = 126,560,553 bp number of sequenced bases = 126,518,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,764 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7064 >>>>>>> ACTG content number of A's = 35,578,794 bp (28.12%) number of C's = 23,841,805 bp (18.84%) number of T's = 38,893,705 bp (30.74%) number of G's = 28,203,161 bp (22.29%) number of N's = 1,412 bp (0%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,025,842 number of insertions = 9,249 mapped reads with insertion percentage = 0.46% number of deletions = 26,156 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.0409X std coverageData = 0.299X There is a 3.57% of reference with a coverageData >= 1X There is a 0.4% 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 10539830 0.04228607318093703 0.4430470614966941 chr2 243199373 10030210 0.04124274613158645 0.3711073617720243 chr3 198022430 8350874 0.042171354022875085 0.2286091379528941 chr4 191154276 8299622 0.043418448039320864 0.23782813269587375 chr5 180915260 8075004 0.04463417845459802 0.23522777155054536 chr6 171115067 7431729 0.04343117838945182 0.2712307898374632 chr7 159138663 6800366 0.04273233086041448 0.3260547636565507 chr8 146364022 6303692 0.043068589629219126 0.2931478202689718 chr9 141213431 5429854 0.03845139914488729 0.2815517843964485 chr10 135534747 5516560 0.040702182444771896 0.3119163120989065 chr11 135006516 6072672 0.044980584492677375 0.28625072303708965 chr12 133851895 5901747 0.04409162081717259 0.2353288549789461 chr13 115169878 4836959 0.0419984728993114 0.23093459650924308 chr14 107349540 3707738 0.03453892769358863 0.21944245450293323 chr15 102531392 3392578 0.033088188249702104 0.20457452501958295 chr16 90354753 3519930 0.03895677740384061 0.24328776313923653 chr17 81195210 3381652 0.041648417437432576 0.24738149967501002 chr18 78077248 3478192 0.04454808653091871 0.5740596439133447 chr19 59128983 2166200 0.03663516417997583 0.3353196431150601 chr20 63025520 2565718 0.04070919208599945 0.23421062048909472 chr21 48129895 1892006 0.03931041195913683 0.22902376950462935 chr22 51304566 1194882 0.023289973839755316 0.16882944993523424 chrMT 16571 97728 5.897531832719812 4.294858607695626 chrX 155270560 7264374 0.0467852630917284 0.2645804620902481 chrY 59373566 310436 0.005228522066537152 0.10770728631396818