BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524316.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 = 2,274,638 number of mapped reads = 2,079,422 (91.42%) number of supplementary alignments = 8,171 (0.36%) number of secondary alignments = 0 number of mapped bases = 121,064,323 bp number of sequenced bases = 121,031,665 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,624 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7129 >>>>>>> ACTG content number of A's = 29,440,191 bp (24.32%) number of C's = 24,031,633 bp (19.86%) number of T's = 37,536,222 bp (31.01%) number of G's = 30,006,947 bp (24.79%) number of N's = 16,672 bp (0.01%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 629,225 number of insertions = 6,789 mapped reads with insertion percentage = 0.32% number of deletions = 20,648 mapped reads with deletion percentage = 0.99% homopolymer indels = 42.91% >>>>>>> Coverage mean coverageData = 0.0391X std coverageData = 0.3591X There is a 3.39% 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 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10184529 0.04086059629115227 0.6532340101711849 chr2 243199373 7859005 0.032315070976766044 0.4984093414782958 chr3 198022430 8182040 0.04131875363816109 0.23131266064671457 chr4 191154276 6220111 0.032539742924714905 0.2386330755291477 chr5 180915260 7003843 0.03871338990420156 0.22172236418386035 chr6 171115067 7568954 0.044233124135117804 0.25835161448719135 chr7 159138663 5577372 0.03504724681518783 0.4677470538659109 chr8 146364022 12443381 0.08501666481944586 0.4585161069953396 chr9 141213431 5028104 0.03560641480341909 0.27924048605612595 chr10 135534747 6140536 0.04530599079511323 0.3682316062563199 chr11 135006516 5806356 0.04300796859316035 0.3101314036237678 chr12 133851895 4764370 0.03559434104388287 0.21687963330410218 chr13 115169878 3085642 0.026792092286491785 0.1854310306631087 chr14 107349540 2548462 0.023739850212679065 0.18591511124643692 chr15 102531392 3716441 0.036246859888530526 0.21357830967680458 chr16 90354753 3907857 0.04325015420052114 0.25422018833480636 chr17 81195210 3748249 0.046163425157715585 0.27233981703834187 chr18 78077248 2835657 0.036318608463249115 0.509534530486375 chr19 59128983 2256351 0.0381598141134949 0.43849730585011704 chr20 63025520 2772240 0.04398599170621678 0.24515081577182224 chr21 48129895 2132840 0.04431424585488915 0.26449590884546725 chr22 51304566 906806 0.01767495703988608 0.14965790238621834 chrMT 16571 4196 0.25321344517530625 0.5571289229413325 chrX 155270560 5993713 0.03860173493288103 0.2532959694535766 chrY 59373566 377268 0.006354140830954974 0.17065008843394025