BamQC report ----------------------------------- >>>>>>> Input bam file = SRR7062654_1.bam outfile = SRR7062654_1/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 = 177,964,907 bp number of sequenced bases = 177,854,525 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 327,476 duplication rate = 16.66% >>>>>>> Insert size mean insert size = 586.9708 std insert size = 11,397.0427 median insert size = 481 >>>>>>> Mapping quality mean mapping quality = 54.6913 >>>>>>> ACTG content number of A's = 43,813,202 bp (24.63%) number of C's = 45,163,359 bp (25.39%) number of T's = 43,752,660 bp (24.6%) number of G's = 45,092,509 bp (25.35%) number of N's = 32,795 bp (0.02%) GC percentage = 50.75% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,698,916 number of insertions = 34,815 mapped reads with insertion percentage = 1.71% number of deletions = 39,461 mapped reads with deletion percentage = 1.9% homopolymer indels = 45.8% >>>>>>> Coverage mean coverageData = 21.65X std coverageData = 11.8152X There is a 90.29% of reference with a coverageData >= 1X There is a 89.24% of reference with a coverageData >= 2X There is a 88.4% of reference with a coverageData >= 3X There is a 87.6% of reference with a coverageData >= 4X There is a 86.8% of reference with a coverageData >= 5X There is a 85.98% of reference with a coverageData >= 6X There is a 85.09% of reference with a coverageData >= 7X There is a 84.18% of reference with a coverageData >= 8X There is a 83.2% of reference with a coverageData >= 9X There is a 82.15% of reference with a coverageData >= 10X There is a 80.97% of reference with a coverageData >= 11X There is a 79.7% of reference with a coverageData >= 12X There is a 78.31% of reference with a coverageData >= 13X There is a 76.78% of reference with a coverageData >= 14X There is a 75.1% of reference with a coverageData >= 15X There is a 73.21% of reference with a coverageData >= 16X There is a 71.11% of reference with a coverageData >= 17X There is a 68.76% of reference with a coverageData >= 18X There is a 66.12% of reference with a coverageData >= 19X There is a 63.23% of reference with a coverageData >= 20X There is a 60.07% of reference with a coverageData >= 21X There is a 56.65% of reference with a coverageData >= 22X There is a 52.99% of reference with a coverageData >= 23X There is a 49.19% of reference with a coverageData >= 24X There is a 45.26% of reference with a coverageData >= 25X There is a 41.3% of reference with a coverageData >= 26X There is a 37.32% of reference with a coverageData >= 27X There is a 33.41% of reference with a coverageData >= 28X There is a 29.65% of reference with a coverageData >= 29X There is a 26.06% of reference with a coverageData >= 30X There is a 22.67% of reference with a coverageData >= 31X There is a 19.52% of reference with a coverageData >= 32X There is a 16.62% of reference with a coverageData >= 33X There is a 14.02% of reference with a coverageData >= 34X There is a 11.73% of reference with a coverageData >= 35X There is a 9.7% of reference with a coverageData >= 36X There is a 7.94% of reference with a coverageData >= 37X There is a 6.44% of reference with a coverageData >= 38X There is a 5.18% of reference with a coverageData >= 39X There is a 4.13% of reference with a coverageData >= 40X There is a 3.26% of reference with a coverageData >= 41X There is a 2.56% of reference with a coverageData >= 42X There is a 2.01% of reference with a coverageData >= 43X There is a 1.57% of reference with a coverageData >= 44X There is a 1.22% of reference with a coverageData >= 45X There is a 0.94% of reference with a coverageData >= 46X There is a 0.74% of reference with a coverageData >= 47X There is a 0.58% of reference with a coverageData >= 48X There is a 0.46% of reference with a coverageData >= 49X There is a 0.37% of reference with a coverageData >= 50X There is a 0.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig 25 2906300 46291538 15.927997109727144 13.429353436345739 26 5313770 131673369 24.779651546830216 9.467107338503608