BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716579.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 = 1,567,868 number of mapped reads = 1,441,498 (91.94%) number of supplementary alignments = 7,565 (0.48%) number of secondary alignments = 0 number of mapped bases = 84,217,704 bp number of sequenced bases = 84,193,079 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,973 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1818 >>>>>>> ACTG content number of A's = 20,245,659 bp (24.05%) number of C's = 16,195,807 bp (19.24%) number of T's = 26,549,026 bp (31.53%) number of G's = 21,201,532 bp (25.18%) number of N's = 1,055 bp (0%) GC percentage = 44.42% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 417,946 number of insertions = 4,469 mapped reads with insertion percentage = 0.31% number of deletions = 15,507 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.68% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2728X There is a 2.47% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6930999 0.027807348973465547 0.36799931365148064 chr2 243199373 8219665 0.03379805177376012 0.31948834213859234 chr3 198022430 6545544 0.03305455851642665 0.2056274949209057 chr4 191154276 4668701 0.024423733006108637 0.17690203276018632 chr5 180915260 4201398 0.02322301612368133 0.16317115955429276 chr6 171115067 4663011 0.02725073298191795 0.19455528869317698 chr7 159138663 5172733 0.03250456490262206 0.6333362418467888 chr8 146364022 6742355 0.04606565813011069 0.2952069095527624 chr9 141213431 3496150 0.024757914139201108 0.2002175072283238 chr10 135534747 3964895 0.0292537160230948 0.3380914379496389 chr11 135006516 2496110 0.01848881131041112 0.18069960934574883 chr12 133851895 3883959 0.029016839843769116 0.20081285447566294 chr13 115169878 2158013 0.018737651176464736 0.14588512051610317 chr14 107349540 2100738 0.019569138349358552 0.15487005590336955 chr15 102531392 1958911 0.019105475521096992 0.15215953681670236 chr16 90354753 2541813 0.028131480808762765 0.18867853975274707 chr17 81195210 3566976 0.043930867350426214 0.23388952564406965 chr18 78077248 1977879 0.02533233497164244 0.2923230537491053 chr19 59128983 1718718 0.029067268077314978 0.34003476760883455 chr20 63025520 1907268 0.03026183679246121 0.19628167113058187 chr21 48129895 861732 0.017904298357600823 0.14809555916806436 chr22 51304566 1305317 0.025442511296168063 0.17168675053824095 chrMT 16571 56639 3.417959085148754 2.7251757279618527 chrX 155270560 2896449 0.01865420592287424 0.16467950879512144 chrY 59373566 181731 0.0030608065548901006 0.07968341185276072