BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173877.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,989,262 number of mapped reads = 1,942,224 (97.64%) number of supplementary alignments = 177,317 (8.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 972,880 number of mapped paired reads (second in pair) = 969,344 number of mapped paired reads (both in pair) = 1,912,134 number of mapped paired reads (singletons) = 30,090 number of mapped bases = 230,694,753 bp number of sequenced bases = 230,561,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,460,908 duplication rate = 63.76% >>>>>>> Insert size mean insert size = 992,475.2808 std insert size = 9,661,702.6689 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.2152 >>>>>>> ACTG content number of A's = 69,593,191 bp (30.18%) number of C's = 44,904,677 bp (19.48%) number of T's = 69,450,602 bp (30.12%) number of G's = 46,609,431 bp (20.22%) number of N's = 3,214 bp (0%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 2,309,204 number of insertions = 25,038 mapped reads with insertion percentage = 1.24% number of deletions = 55,375 mapped reads with deletion percentage = 2.79% homopolymer indels = 43.2% >>>>>>> Coverage mean coverageData = 0.0745X std coverageData = 1.1981X There is a 1.71% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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% 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 18480120 0.07414272400147802 0.8833506523867347 chr2 243199373 20249006 0.08326093011761178 3.193605319054393 chr3 198022430 15177433 0.0766450194556243 0.7800602103384366 chr4 191154276 15582615 0.08151852695149754 0.8985680440682982 chr5 180915260 14266527 0.07885751041675533 0.7928766595757094 chr6 171115067 14276930 0.08343467498393932 0.8355992760015538 chr7 159138663 12923043 0.08120618054960031 0.87182341290351 chr8 146364022 11635533 0.07949722097688734 0.910171965213025 chr9 141213431 10244005 0.07254271019022263 0.8937181594825861 chr10 135534747 11517156 0.08497567048249258 1.0485066047719784 chr11 135006516 10345100 0.0766266718563421 0.7798394094450565 chr12 133851895 10834963 0.08094740085674544 0.795519085900803 chr13 115169878 8226139 0.07142613279489625 0.7553755467073975 chr14 107349540 7193553 0.0670105619455845 0.7168513546874049 chr15 102531392 6545505 0.06383903380537348 0.6921631027837907 chr16 90354753 6447675 0.07135955537391597 0.7957552085384195 chr17 81195210 6383100 0.07861424337716473 0.7728163156588632 chr18 78077248 6594046 0.08445541010871695 1.095054810476625 chr19 59128983 4035039 0.06824130562164413 0.8054904918658686 chr20 63025520 5068858 0.08042548478774947 0.7942847226050762 chr21 48129895 3331482 0.06921855948366394 0.8559109103539498 chr22 51304566 2804396 0.054661723480908114 0.6479054142905921 chrMT 16571 425919 25.702673345000303 22.77912106852177 chrX 155270560 6535640 0.042091945826691166 0.5742147917612764 chrY 59373566 1570970 0.026459081133850038 0.49047208446483104