BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717012.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 = 1,246,144 number of mapped reads = 1,154,083 (92.61%) number of supplementary alignments = 19,226 (1.54%) number of secondary alignments = 0 number of mapped bases = 91,539,483 bp number of sequenced bases = 91,500,770 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,371 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.295 >>>>>>> ACTG content number of A's = 23,211,908 bp (25.37%) number of C's = 17,365,661 bp (18.98%) number of T's = 27,806,653 bp (30.39%) number of G's = 23,110,804 bp (25.26%) number of N's = 5,744 bp (0.01%) GC percentage = 44.24% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 739,123 number of insertions = 9,268 mapped reads with insertion percentage = 0.79% number of deletions = 22,144 mapped reads with deletion percentage = 1.89% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.3904X There is a 2.62% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 8097996 0.032489371410633315 0.6200739207744664 chr2 243199373 8308739 0.03416431094170625 0.6980867563180686 chr3 198022430 7204284 0.03638115136754962 0.21386313521728448 chr4 191154276 3940144 0.020612376989149854 0.16358644037005166 chr5 180915260 5460508 0.030182683318145744 0.19361033511158585 chr6 171115067 6561323 0.03834450767564495 0.2550730476996697 chr7 159138663 4746852 0.029828401913870546 0.49124251537092234 chr8 146364022 6564756 0.04485225201040185 0.5298511248891835 chr9 141213431 4080678 0.02889723711903863 0.3927416065381357 chr10 135534747 4448280 0.03282021841970901 0.3454008462299353 chr11 135006516 3690739 0.027337487917990566 0.27898311584009877 chr12 133851895 3455936 0.025819104017914724 0.18044369111320888 chr13 115169878 3190723 0.027704492315256252 0.18061640266174012 chr14 107349540 2163479 0.020153593578509977 0.19285782269195606 chr15 102531392 1773490 0.017297044011652548 0.1441211865963259 chr16 90354753 2380858 0.02635011353525586 0.2180187479695208 chr17 81195210 2786684 0.03432079306156114 0.24329349032569608 chr18 78077248 2835850 0.03632108037414433 0.7524323435750883 chr19 59128983 1799843 0.030439268674720823 0.5108219699552905 chr20 63025520 1696433 0.026916604575416433 0.21594053182903253 chr21 48129895 1830232 0.038026926923484874 0.2194486485182065 chr22 51304566 1405103 0.02738748438101981 0.18423278479330082 chrMT 16571 2784 0.16800434493995534 0.4198436105947619 chrX 155270560 2910939 0.018747526897565127 0.2078160393490076 chrY 59373566 202830 0.003416166716346463 0.09169775587956132