BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004104.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 = 2,424,497 number of mapped reads = 1,647,986 (67.97%) number of supplementary alignments = 9,584 (0.4%) number of secondary alignments = 0 number of mapped bases = 106,476,183 bp number of sequenced bases = 106,416,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,749 duplication rate = 7.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8117 >>>>>>> ACTG content number of A's = 28,140,414 bp (26.44%) number of C's = 19,377,339 bp (18.21%) number of T's = 34,727,780 bp (32.63%) number of G's = 24,157,735 bp (22.7%) number of N's = 13,382 bp (0.01%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 1,188,425 number of insertions = 9,354 mapped reads with insertion percentage = 0.56% number of deletions = 36,142 mapped reads with deletion percentage = 2.16% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.0344X std coverageData = 0.3624X There is a 2.38% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 8996123 0.036092680386942744 0.5610595374109831 chr2 243199373 8577791 0.03527061313599686 0.40029402173678535 chr3 198022430 6608748 0.03337373448048284 0.25479773219418816 chr4 191154276 7448857 0.03896777595495693 0.2857717463831112 chr5 180915260 6009460 0.03321698788703618 0.25426331926532336 chr6 171115067 6403049 0.03741955113748107 0.29359900074901124 chr7 159138663 7478888 0.04699604646043809 0.6844662183958018 chr8 146364022 6378811 0.04358182368068568 0.36424589793019674 chr9 141213431 3647977 0.02583307390923743 0.30318538239766973 chr10 135534747 5042431 0.037203972498653794 0.3413573770510457 chr11 135006516 4454953 0.032998059145530424 0.33051648328046473 chr12 133851895 4568252 0.03412915446583704 0.26266951186683 chr13 115169878 3136433 0.027233101696955867 0.2340568711465799 chr14 107349540 2752838 0.025643686968756456 0.234235555493673 chr15 102531392 2968492 0.028952030613219413 0.24003492730756681 chr16 90354753 3006746 0.033277120463159254 0.2638796921903422 chr17 81195210 2599813 0.032019290300499256 0.2702253195875301 chr18 78077248 3065032 0.03925640411916158 0.5507330736115739 chr19 59128983 1853232 0.03134219304938832 0.36769685005398683 chr20 63025520 2573992 0.04084047224045117 0.2934548044467563 chr21 48129895 1475322 0.030652923718200508 0.25444767950905334 chr22 51304566 1146220 0.022341481263090695 0.20310474746030097 chrMT 16571 88205 5.322853177237342 4.861645008168726 chrX 155270560 5903133 0.03801836613457181 0.29055605818148483 chrY 59373566 291385 0.004907655369731372 0.11086970455069078