BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084964.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 = 2,639,103 number of mapped reads = 2,370,750 (89.83%) number of supplementary alignments = 23,587 (0.89%) number of secondary alignments = 0 number of mapped bases = 157,407,938 bp number of sequenced bases = 157,348,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,723 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0958 >>>>>>> ACTG content number of A's = 43,912,910 bp (27.91%) number of C's = 29,135,103 bp (18.52%) number of T's = 49,264,347 bp (31.31%) number of G's = 35,015,482 bp (22.25%) number of N's = 20,906 bp (0.01%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,344,387 number of insertions = 12,632 mapped reads with insertion percentage = 0.53% number of deletions = 36,736 mapped reads with deletion percentage = 1.53% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.0508X std coverageData = 0.501X There is a 4.44% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12416162 0.04981396616058983 0.887911677843621 chr2 243199373 13504254 0.055527503354213005 0.6215397633668539 chr3 198022430 10974029 0.05541811096854028 0.26950546978736606 chr4 191154276 9545714 0.04993722452748062 0.26096320056759303 chr5 180915260 9719776 0.053725572956090054 0.262505985207412 chr6 171115067 9668795 0.056504638483997435 0.4177671906794223 chr7 159138663 8796957 0.05527856546086478 0.5077048603307276 chr8 146364022 8164875 0.055784713267854856 0.6730919450840229 chr9 141213431 7016274 0.04968559966509135 0.5299134068097753 chr10 135534747 6725069 0.04961878152175988 0.5480129603782303 chr11 135006516 6848662 0.05072838113976662 0.4320526885776855 chr12 133851895 7297875 0.05452201479852041 0.2785069228074266 chr13 115169878 5234135 0.04544708296035531 0.23395825971806444 chr14 107349540 4874933 0.04541177353903892 0.2969917269902757 chr15 102531392 4578685 0.04465642093301533 0.23961704860217134 chr16 90354753 4483245 0.04961825306522613 0.3228600377282828 chr17 81195210 4101059 0.05050863222103866 0.31049582232406214 chr18 78077248 4031142 0.051630175284866596 1.0845287803469372 chr19 59128983 2787736 0.04714669284942716 0.7351735036237038 chr20 63025520 3086454 0.04897149599083038 0.262040751589119 chr21 48129895 1960651 0.04073665650008171 0.2601618520700056 chr22 51304566 1549891 0.030209611362856086 0.18981363119189867 chrMT 16571 27776 1.676181280550359 1.7160748333096434 chrX 155270560 9627527 0.06200484496223882 0.36052021624369723 chrY 59373566 386262 0.006505622384210509 0.12739225951660224