BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714053.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 487,384 number of mapped reads = 79,678 (16.35%) number of supplementary alignments = 2,719 (0.56%) number of secondary alignments = 0 number of mapped bases = 8,197,980 bp number of sequenced bases = 8,177,669 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,988 duplication rate = 24.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 17.3005 >>>>>>> ACTG content number of A's = 282,592 bp (3.46%) number of C's = 110,281 bp (1.35%) number of T's = 143,572 bp (1.76%) number of G's = 7,641,033 bp (93.44%) number of N's = 191 bp (0%) GC percentage = 94.79% >>>>>>> Mismatches and indels general error rate = 0.0326 number of mismatches = 199,910 number of insertions = 9,359 mapped reads with insertion percentage = 7.55% number of deletions = 4,462 mapped reads with deletion percentage = 5.31% homopolymer indels = 65.25% >>>>>>> Coverage mean coverageData = 0.0026X std coverageData = 9.781X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 37385 1.4998959621448648E-4 0.25672932776886354 chr2 243199373 7629073 0.031369624460339376 34.89339854346522 chr3 198022430 15724 7.940514617460255E-5 0.015045671789933856 chr4 191154276 17969 9.400260551848706E-5 0.03902123253783986 chr5 180915260 10079 5.571116554789242E-5 0.010461643370699962 chr6 171115067 13709 8.011568028664595E-5 0.02822800049237842 chr7 159138663 22040 1.3849557099772795E-4 0.08587117403800879 chr8 146364022 23276 1.5902815242396112E-4 0.04874020054862474 chr9 141213431 7439 5.267912511806331E-5 0.012879204579440643 chr10 135534747 32094 2.3679536584076113E-4 0.3466204866344751 chr11 135006516 10932 8.097386943901285E-5 0.030388609883631647 chr12 133851895 24511 1.8312030621606067E-4 0.1362352375967205 chr13 115169878 6541 5.679436423471769E-5 0.01048392499461864 chr14 107349540 11057 1.029999755937473E-4 0.0829676077354418 chr15 102531392 8431 8.222847496306302E-5 0.03065175341279384 chr16 90354753 6633 7.34106372909901E-5 0.01430459251175466 chr17 81195210 13351 1.6443088206804317E-4 0.14183730993493635 chr18 78077248 4549 5.82628117220525E-5 0.012591454129388589 chr19 59128983 4057 6.86127140052451E-5 0.02161702432764465 chr20 63025520 6039 9.58183288293377E-5 0.03572155488714067 chr21 48129895 1897 3.9414172833745016E-5 0.008231198573200768 chr22 51304566 2350 4.580488995852728E-5 0.00869512560536281 chrMT 16571 5824 0.3514573652766882 2.1346223480611353 chrX 155270560 280121 0.0018040831436429417 0.26075553038783694 chrY 59373566 2899 4.882644239357292E-5 0.018721385982375376