BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716411.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 = 1,030,562 number of mapped reads = 839,119 (81.42%) number of supplementary alignments = 4,024 (0.39%) number of secondary alignments = 0 number of mapped bases = 48,590,906 bp number of sequenced bases = 48,577,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,222 duplication rate = 1.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4598 >>>>>>> ACTG content number of A's = 12,822,259 bp (26.4%) number of C's = 8,784,746 bp (18.08%) number of T's = 15,131,595 bp (31.15%) number of G's = 11,837,829 bp (24.37%) number of N's = 789 bp (0%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 239,288 number of insertions = 4,010 mapped reads with insertion percentage = 0.48% number of deletions = 8,731 mapped reads with deletion percentage = 1.03% homopolymer indels = 41.86% >>>>>>> Coverage mean coverageData = 0.0157X std coverageData = 0.1624X There is a 1.46% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 5259503 0.021101263374585535 0.22585653757821858 chr2 243199373 4207628 0.017301146578202732 0.2105623444348385 chr3 198022430 3869403 0.019540225821893006 0.14748857315250266 chr4 191154276 2359818 0.012345096585754639 0.12352950261213945 chr5 180915260 2180791 0.012054212563384648 0.11588590944641589 chr6 171115067 4271969 0.024965475424791203 0.20816377980247566 chr7 159138663 2789016 0.01752569707086203 0.20621977994633006 chr8 146364022 3507144 0.02396179028204076 0.17221409942560967 chr9 141213431 2071195 0.014667124687311081 0.15104702876087586 chr10 135534747 2454343 0.018108588788674242 0.17499573648268046 chr11 135006516 1627446 0.012054573721463933 0.13765787871817725 chr12 133851895 2161999 0.01615217326583236 0.13633550324864224 chr13 115169878 1133175 0.00983916124318548 0.1044878121794024 chr14 107349540 1069723 0.009964858722263738 0.11318272529530493 chr15 102531392 1036281 0.010106963143541443 0.10627733237608765 chr16 90354753 1055813 0.01168519601840979 0.12353192601453676 chr17 81195210 1167455 0.014378372812878987 0.12869292124146797 chr18 78077248 942552 0.0120720443425465 0.21222411342548103 chr19 59128983 766149 0.01295724974671051 0.16442245258330163 chr20 63025520 857808 0.0136104866727002 0.12343721077901593 chr21 48129895 457990 0.009515707441289867 0.11438217130298538 chr22 51304566 615068 0.011988562577451683 0.1152038321857464 chrMT 16571 8834 0.5330999939653611 0.8584109044449925 chrX 155270560 2600608 0.01674888014830371 0.14598524112942884 chrY 59373566 119195 0.002007543222180726 0.060365227381356426