BamQC report ----------------------------------- >>>>>>> Input bam file = SRR23117301.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP418207/SRP418207.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 = 165,182 number of mapped reads = 157,841 (95.56%) number of supplementary alignments = 654 (0.4%) number of secondary alignments = 0 number of mapped bases = 36,794,033 bp number of sequenced bases = 36,722,417 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,467 duplication rate = 10.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 53.5861 >>>>>>> ACTG content number of A's = 10,804,004 bp (29.42%) number of C's = 7,565,748 bp (20.6%) number of T's = 10,717,701 bp (29.19%) number of G's = 7,634,964 bp (20.79%) number of N's = 0 bp (0%) GC percentage = 41.39% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 185,546 number of insertions = 172,474 mapped reads with insertion percentage = 48.21% number of deletions = 58,574 mapped reads with deletion percentage = 25.65% homopolymer indels = 30.78% >>>>>>> Coverage mean coverageData = 0.0119X std coverageData = 0.2457X There is a 1.01% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 3145600 0.012620229339368426 0.708231734515807 chr2 243199373 3177725 0.013066337140597808 0.13225702782165533 chr3 198022430 2602532 0.013142612177822482 0.13150213365235972 chr4 191154276 2528768 0.01322893765661826 0.13449701091065083 chr5 180915260 2301631 0.012722149585391525 0.12835721498218028 chr6 171115067 2200693 0.01286089552827046 0.129407866463677 chr7 159138663 1999714 0.01256585899556037 0.30913871279626215 chr8 146364022 1879977 0.012844529511494293 0.13022494831554202 chr9 141213431 1517838 0.010748538501270463 0.12127874735317405 chr10 135534747 1744656 0.012872389100338971 0.16710131473156092 chr11 135006516 1628518 0.012062514078950086 0.126812325570072 chr12 133851895 1647684 0.01230975474796229 0.1279465562633086 chr13 115169878 1243418 0.010796382019263752 0.1183524699064518 chr14 107349540 1069199 0.00995997747172461 0.11388502193746793 chr15 102531392 1085521 0.01058720630653293 0.11760951781267046 chr16 90354753 977379 0.010817128790114672 0.13261432998152697 chr17 81195210 816660 0.010057982484434734 0.11687364475603876 chr18 78077248 1018758 0.013048077719132724 0.13696038039743463 chr19 59128983 494428 0.008361855301992934 0.2125033428436777 chr20 63025520 741952 0.011772247178603206 0.1284325117324155 chr21 48129895 491220 0.010206130721872549 0.120109430900843 chr22 51304566 344761 0.006719889219996521 0.09386307852092572 chrMT 16571 40570 2.4482529720596222 5.688315931481862 chrX 155270560 2051015 0.013209297370989066 0.1314470522759895 chrY 59373566 43816 7.379715073876479E-4 0.048061405069282526