BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714151.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 = 747,678 number of mapped reads = 597,683 (79.94%) number of supplementary alignments = 14,400 (1.93%) number of secondary alignments = 0 number of mapped bases = 77,684,699 bp number of sequenced bases = 75,849,688 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 538,081 duplication rate = 45.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.2936 >>>>>>> ACTG content number of A's = 19,904,990 bp (26.24%) number of C's = 16,882,771 bp (22.26%) number of T's = 19,009,051 bp (25.06%) number of G's = 20,052,280 bp (26.44%) number of N's = 596 bp (0%) GC percentage = 48.7% >>>>>>> Mismatches and indels general error rate = 0.0452 number of mismatches = 3,238,141 number of insertions = 77,688 mapped reads with insertion percentage = 12.49% number of deletions = 287,057 mapped reads with deletion percentage = 45.65% homopolymer indels = 28.17% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 10.1066X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7656647 0.030718667697923207 8.271526268632533 chr2 243199373 11295765 0.04644652188309713 17.084809975829472 chr3 198022430 2560404 0.012929868601248859 2.846516997673705 chr4 191154276 2557157 0.013377451205956806 3.148528896463851 chr5 180915260 3326599 0.018387608651696932 3.825252232229924 chr6 171115067 2826086 0.01651570518918711 3.1792231727059215 chr7 159138663 1947342 0.012236762351082465 2.1238856776295134 chr8 146364022 3122613 0.02133456676942097 9.514543483764061 chr9 141213431 3466913 0.02455087292652779 6.4638941927118765 chr10 135534747 3239826 0.02390402514271857 3.953489259192657 chr11 135006516 3272910 0.02424260766791434 4.141362896239656 chr12 133851895 3700940 0.027649515160020708 4.994736218878981 chr13 115169878 2048368 0.01778562273027675 5.4248095660110796 chr14 107349540 7230795 0.0673574847176802 40.1558863980626 chr15 102531392 2505932 0.02444063180181929 4.241504493745486 chr16 90354753 1387976 0.01536140550348248 1.8000152556055407 chr17 81195210 2647224 0.03260320405600281 7.126151736588386 chr18 78077248 1879867 0.02407701408738177 4.9428570078819165 chr19 59128983 1618302 0.027369014616740493 3.1398558113467665 chr20 63025520 2595006 0.041173892734244794 8.628310224916925 chr21 48129895 628168 0.013051514033014201 2.2774865743520034 chr22 51304566 453099 0.008831553121412235 1.2856086614130748 chrMT 16571 255423 15.413855530746485 131.29659785909163 chrX 155270560 4909796 0.031620907401892544 3.5347890952714174 chrY 59373566 551541 0.009289335931077477 1.5747722297189493