BamQC report ----------------------------------- >>>>>>> Input bam file = SRR7062654.recal.bam outfile = SRR7062654.recal/genome_results.txt >>>>>>> Reference number of bases = 8,220,070 bp number of contigs = 2 >>>>>>> Globals number of windows = 401 number of reads = 1,987,908 number of mapped reads = 1,986,265 (99.92%) number of secondary alignments = 698 number of mapped paired reads (first in pair) = 993,166 number of mapped paired reads (second in pair) = 993,099 number of mapped paired reads (both in pair) = 1,984,622 number of mapped paired reads (singletons) = 1,643 number of mapped bases = 173,004,946 bp number of sequenced bases = 172,897,471 bp number of aligned bases = 0 bp number of duplicated reads (flagged) = 55,440 >>>>>>> Insert size mean insert size = 588.4926 std insert size = 11,533.6506 median insert size = 482 >>>>>>> Mapping quality mean mapping quality = 54.6838 >>>>>>> ACTG content number of A's = 42,569,790 bp (24.62%) number of C's = 43,925,775 bp (25.41%) number of T's = 42,512,566 bp (24.59%) number of G's = 43,857,858 bp (25.37%) number of N's = 31,482 bp (0.02%) GC percentage = 50.77% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,642,825 number of insertions = 33,851 mapped reads with insertion percentage = 1.66% number of deletions = 38,353 mapped reads with deletion percentage = 1.85% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 21.0467X std coverageData = 11.4076X There is a 90.29% of reference with a coverageData >= 1X There is a 89.23% of reference with a coverageData >= 2X There is a 88.39% of reference with a coverageData >= 3X There is a 87.58% of reference with a coverageData >= 4X There is a 86.76% of reference with a coverageData >= 5X There is a 85.92% of reference with a coverageData >= 6X There is a 85.01% of reference with a coverageData >= 7X There is a 84.08% of reference with a coverageData >= 8X There is a 83.07% of reference with a coverageData >= 9X There is a 81.96% of reference with a coverageData >= 10X There is a 80.74% of reference with a coverageData >= 11X There is a 79.41% of reference with a coverageData >= 12X There is a 77.95% of reference with a coverageData >= 13X There is a 76.34% of reference with a coverageData >= 14X There is a 74.56% of reference with a coverageData >= 15X There is a 72.55% of reference with a coverageData >= 16X There is a 70.28% of reference with a coverageData >= 17X There is a 67.74% of reference with a coverageData >= 18X There is a 64.9% of reference with a coverageData >= 19X There is a 61.76% of reference with a coverageData >= 20X There is a 58.33% of reference with a coverageData >= 21X There is a 54.66% of reference with a coverageData >= 22X There is a 50.74% of reference with a coverageData >= 23X There is a 46.69% of reference with a coverageData >= 24X There is a 42.57% of reference with a coverageData >= 25X There is a 38.44% of reference with a coverageData >= 26X There is a 34.35% of reference with a coverageData >= 27X There is a 30.36% of reference with a coverageData >= 28X There is a 26.58% of reference with a coverageData >= 29X There is a 23.01% of reference with a coverageData >= 30X There is a 19.68% of reference with a coverageData >= 31X There is a 16.67% of reference with a coverageData >= 32X There is a 13.95% of reference with a coverageData >= 33X There is a 11.55% of reference with a coverageData >= 34X There is a 9.44% of reference with a coverageData >= 35X There is a 7.63% of reference with a coverageData >= 36X There is a 6.11% of reference with a coverageData >= 37X There is a 4.84% of reference with a coverageData >= 38X There is a 3.81% of reference with a coverageData >= 39X There is a 2.97% of reference with a coverageData >= 40X There is a 2.3% of reference with a coverageData >= 41X There is a 1.77% of reference with a coverageData >= 42X There is a 1.36% of reference with a coverageData >= 43X There is a 1.04% of reference with a coverageData >= 44X There is a 0.8% of reference with a coverageData >= 45X There is a 0.61% of reference with a coverageData >= 46X There is a 0.48% of reference with a coverageData >= 47X There is a 0.39% of reference with a coverageData >= 48X There is a 0.32% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig 25 2906300 45027010 15.492898186697863 12.985154788982253 26 5313770 127977936 24.084206881366715 9.110699911878513