BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716397.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 = 1,428,139 number of mapped reads = 1,291,403 (90.43%) number of supplementary alignments = 20,803 (1.46%) number of secondary alignments = 0 number of mapped bases = 100,972,955 bp number of sequenced bases = 100,928,433 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,869 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3741 >>>>>>> ACTG content number of A's = 25,179,725 bp (24.95%) number of C's = 19,936,327 bp (19.75%) number of T's = 31,042,919 bp (30.76%) number of G's = 24,763,732 bp (24.54%) number of N's = 5,730 bp (0.01%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 879,885 number of insertions = 10,350 mapped reads with insertion percentage = 0.79% number of deletions = 25,480 mapped reads with deletion percentage = 1.94% homopolymer indels = 43.28% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.4649X There is a 2.86% of reference with a coverageData >= 1X There is a 0.24% 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 0.01% 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 10368406 0.04159831561663391 0.8273967071827039 chr2 243199373 9431763 0.03878202021515902 0.784094204244715 chr3 198022430 6918819 0.034939572249466894 0.22994268250423103 chr4 191154276 3971045 0.020774031756422756 0.16766497574349412 chr5 180915260 5851927 0.03234623215310859 0.19979262250556462 chr6 171115067 7038885 0.04113538990695659 0.2873468067812698 chr7 159138663 6849556 0.04304143236392529 0.6450942139060785 chr8 146364022 6485718 0.04431224225308594 0.5757783342389129 chr9 141213431 4304378 0.030481364056652655 0.4066416877269168 chr10 135534747 5254314 0.03876728378738185 0.6424787816472498 chr11 135006516 3747646 0.027759000906296998 0.29898507658290635 chr12 133851895 3930937 0.029367809846846022 0.19389018908651412 chr13 115169878 2721874 0.023633558073231614 0.16672149337792022 chr14 107349540 2331818 0.021721732575658917 0.19245814021934343 chr15 102531392 2220668 0.021658420476725802 0.17000934439677254 chr16 90354753 2910693 0.032214055191983094 0.23285169734403768 chr17 81195210 3322253 0.04091685950439687 0.2637022482722993 chr18 78077248 2309372 0.029578040455524254 0.6816071667218997 chr19 59128983 2049172 0.034655965586284476 0.6767181223306363 chr20 63025520 1731558 0.027473918501584756 0.19662263120915816 chr21 48129895 1474575 0.030637403218934926 0.1996973264291448 chr22 51304566 1185421 0.023105565301926537 0.16782547167318942 chrMT 16571 46880 2.8290386820348803 2.5233126385987243 chrX 155270560 4270775 0.027505375133573293 0.24883178509542692 chrY 59373566 244502 0.004118027877928033 0.11477766587399042