BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236065.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,445,839 number of mapped reads = 1,298,844 (89.83%) number of supplementary alignments = 5,583 (0.39%) number of secondary alignments = 0 number of mapped bases = 87,220,260 bp number of sequenced bases = 87,183,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,733 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5135 >>>>>>> ACTG content number of A's = 24,152,348 bp (27.7%) number of C's = 15,778,351 bp (18.1%) number of T's = 27,874,372 bp (31.97%) number of G's = 19,326,291 bp (22.17%) number of N's = 51,783 bp (0.06%) GC percentage = 40.27% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 697,590 number of insertions = 6,632 mapped reads with insertion percentage = 0.51% number of deletions = 21,068 mapped reads with deletion percentage = 1.61% homopolymer indels = 49.22% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.2771X There is a 2.46% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 5933910 0.0238070018690144 0.36189972691100136 chr2 243199373 5420130 0.02228677620809491 0.36305520138784897 chr3 198022430 4881070 0.02464907636978296 0.17339583223607624 chr4 191154276 3755229 0.019645016991406458 0.16856686168565002 chr5 180915260 5064441 0.02799344289696734 0.18643087519254692 chr6 171115067 5957647 0.03481661261307866 0.23874401504562193 chr7 159138663 5687450 0.03573895804315008 0.36742569159473826 chr8 146364022 5485096 0.03747571243976884 0.4304590861500907 chr9 141213431 3778708 0.026758842790244222 0.3061741794374142 chr10 135534747 3762607 0.0277611983884841 0.22593178774941797 chr11 135006516 4408011 0.03265035740941571 0.2741116667334363 chr12 133851895 3007941 0.022472158500258813 0.17021286157572693 chr13 115169878 2902509 0.02520198033030824 0.17567971656401418 chr14 107349540 2864056 0.026679723080322466 0.19523228060316758 chr15 102531392 2416473 0.023568128286018 0.17637851803104795 chr16 90354753 2722716 0.030133622300976243 0.20988285926190764 chr17 81195210 3026773 0.03727772857536793 0.23213045178664446 chr18 78077248 4075512 0.05219845863419776 0.5501187448503966 chr19 59128983 1995791 0.03375317650905648 0.29562200751674106 chr20 63025520 2113642 0.03353628815755903 0.21155785668091903 chr21 48129895 1563404 0.03248301289666225 0.21536465241101233 chr22 51304566 1067954 0.020815964021603846 0.15970221799591633 chrMT 16571 44224 2.6687586747933136 2.3127978603923225 chrX 155270560 5052673 0.03254108827842187 0.21828050737680962 chrY 59373566 232293 0.003912397648475417 0.10061272359310344