BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083671.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 = 1,154,485 number of mapped reads = 907,024 (78.57%) number of supplementary alignments = 6,932 (0.6%) number of secondary alignments = 0 number of mapped bases = 60,214,946 bp number of sequenced bases = 60,193,752 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,740 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2719 >>>>>>> ACTG content number of A's = 18,482,141 bp (30.7%) number of C's = 11,130,168 bp (18.49%) number of T's = 17,746,921 bp (29.48%) number of G's = 12,830,784 bp (21.32%) number of N's = 3,738 bp (0.01%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 562,488 number of insertions = 4,593 mapped reads with insertion percentage = 0.5% number of deletions = 13,281 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.0195X std coverageData = 0.1921X There is a 1.82% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 6525543 0.02618064891401013 0.3966513134810598 chr2 243199373 6583148 0.027068934918676783 0.19521147322422971 chr3 198022430 5570109 0.02812867714026133 0.17677254196834485 chr4 191154276 2785563 0.014572329001941865 0.12644526047005078 chr5 180915260 3108200 0.017180419164198754 0.13721087740277366 chr6 171115067 3586041 0.02095689796854651 0.1668145555079888 chr7 159138663 2489319 0.015642452645212936 0.16041907681765494 chr8 146364022 4250413 0.029040012305756396 0.25227728345316636 chr9 141213431 2658919 0.018829080075251484 0.15514701745887727 chr10 135534747 2997927 0.022119250349875223 0.19205458080564933 chr11 135006516 2189268 0.016216017306897985 0.14430339752211727 chr12 133851895 2135715 0.015955806976061117 0.13251898260536957 chr13 115169878 2148256 0.0186529328441244 0.1422120124543476 chr14 107349540 1413675 0.013168896671564685 0.12089233871893712 chr15 102531392 1604245 0.015646378818303764 0.13048487222414168 chr16 90354753 1724567 0.01908662181833423 0.14747972483354438 chr17 81195210 1160424 0.014291779034748478 0.1311003146840842 chr18 78077248 1632090 0.02090352877191573 0.22349856556466 chr19 59128983 1327226 0.02244628492933829 0.24269101784335687 chr20 63025520 979215 0.015536801600367597 0.13193164770915877 chr21 48129895 743158 0.015440673618756076 0.13047744699971597 chr22 51304566 408704 0.00796623053004678 0.09270628672783698 chrMT 16571 3706 0.2236437149236618 0.4692703010443052 chrX 155270560 2084591 0.01342553926513822 0.12389853816914444 chrY 59373566 104924 0.0017671837329090187 0.048917234185265994