BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716662.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 = 1,655,587 number of mapped reads = 1,545,655 (93.36%) number of supplementary alignments = 27,820 (1.68%) number of secondary alignments = 0 number of mapped bases = 123,469,183 bp number of sequenced bases = 123,413,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,452 duplication rate = 2.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8947 >>>>>>> ACTG content number of A's = 31,504,151 bp (25.53%) number of C's = 24,907,664 bp (20.18%) number of T's = 37,258,355 bp (30.19%) number of G's = 29,734,719 bp (24.09%) number of N's = 8,917 bp (0.01%) GC percentage = 44.28% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 795,748 number of insertions = 9,795 mapped reads with insertion percentage = 0.62% number of deletions = 28,843 mapped reads with deletion percentage = 1.84% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.0399X std coverageData = 0.3452X There is a 3.47% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% 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 10004363 0.040137765594573986 0.6098009237998661 chr2 243199373 10362467 0.04260893797616822 0.40526350415819573 chr3 198022430 8066985 0.04073773359916854 0.22360898230916898 chr4 191154276 7983355 0.04176393626685076 0.27474913461872474 chr5 180915260 7507996 0.04150007025388571 0.22846863140855145 chr6 171115067 7069531 0.04131448576646965 0.24764627331107397 chr7 159138663 6800014 0.04273011895292849 0.461743375534105 chr8 146364022 6021384 0.04113978228884691 0.40614052597300326 chr9 141213431 5210206 0.036895966361726595 0.3103757125282124 chr10 135534747 5956986 0.04395172553057557 0.3673544817474112 chr11 135006516 5689400 0.042141669665781166 0.33021128529892874 chr12 133851895 5478380 0.040928669706170394 0.22568557766326672 chr13 115169878 3958720 0.03437287656065764 0.20537033139042582 chr14 107349540 3832323 0.03569948227072049 0.22326517534343976 chr15 102531392 3615771 0.035265014250464875 0.20848322443387104 chr16 90354753 3633826 0.04021731983485141 0.2395545292558247 chr17 81195210 3421214 0.0421356629288846 0.2509459042424511 chr18 78077248 3246463 0.04158014124678165 0.5168655872005502 chr19 59128983 2492308 0.042150361354938236 0.4543540535258454 chr20 63025520 2720447 0.04316421348050758 0.24372987121771258 chr21 48129895 1654629 0.03437840452384116 0.23599987239189432 chr22 51304566 1403959 0.02736518617075915 0.18617375226303404 chrMT 16571 6578 0.3969585420312594 0.6716138411516563 chrX 155270560 6961190 0.04483264567346186 0.271968740596504 chrY 59373566 370688 0.00624331710175535 0.21475621507314605