BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716390.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,847,365 number of mapped reads = 1,652,263 (89.44%) number of supplementary alignments = 27,018 (1.46%) number of secondary alignments = 0 number of mapped bases = 128,666,637 bp number of sequenced bases = 128,611,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,770 duplication rate = 2.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6591 >>>>>>> ACTG content number of A's = 32,662,519 bp (25.4%) number of C's = 24,592,681 bp (19.12%) number of T's = 38,925,652 bp (30.27%) number of G's = 32,423,469 bp (25.21%) number of N's = 7,558 bp (0.01%) GC percentage = 44.33% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,140,745 number of insertions = 12,727 mapped reads with insertion percentage = 0.76% number of deletions = 31,788 mapped reads with deletion percentage = 1.9% homopolymer indels = 43.89% >>>>>>> Coverage mean coverageData = 0.0416X std coverageData = 0.5596X There is a 3.54% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.07% 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% 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 10479734 0.042044966459682365 0.8222606034742796 chr2 243199373 11598393 0.047690883643848866 1.0176196094483552 chr3 198022430 9874547 0.04986580055602792 0.26262515322212565 chr4 191154276 5436156 0.028438579108740418 0.20557035277784688 chr5 180915260 7209465 0.039849955166855466 0.2356118386308246 chr6 171115067 7792265 0.04553815824996872 0.31266009130898675 chr7 159138663 7524586 0.04728320483627539 0.8142046413643983 chr8 146364022 8329407 0.0569088419830387 0.7640275913176161 chr9 141213431 5774151 0.04088953125145724 0.5565325842199073 chr10 135534747 6228088 0.045951965365752294 0.4292668993310808 chr11 135006516 5141130 0.03808060642050788 0.3796596505632053 chr12 133851895 4915097 0.036720414006839425 0.22732571047323097 chr13 115169878 5139106 0.04462196269757271 0.2392694586887319 chr14 107349540 3515727 0.03275027540872555 0.2756068873631522 chr15 102531392 2592013 0.02528018931021633 0.1855160586877036 chr16 90354753 3321204 0.036757380101520506 0.2741592671841163 chr17 81195210 4025835 0.04958217362822265 0.3078325906630926 chr18 78077248 3973724 0.05089477538962439 1.2588328256103856 chr19 59128983 2609026 0.04412431717284906 0.6544399933524604 chr20 63025520 2318081 0.03678003767362808 0.2787166518968675 chr21 48129895 2771976 0.05759364320242128 0.2884055547917952 chr22 51304566 2188062 0.04264848473720643 0.23642476444205054 chrMT 16571 125993 7.6032224971335465 5.235314343881835 chrX 155270560 5476788 0.035272546192916414 0.3430749202951984 chrY 59373566 306083 0.005155206611642629 0.14089146256621354