BamQC report ----------------------------------- >>>>>>> Input bam file = SRR7062655.recal.bam outfile = SRR7062655.recal/genome_results.txt >>>>>>> Reference number of bases = 8,220,070 bp number of contigs = 2 >>>>>>> Globals number of windows = 401 number of reads = 1,921,198 number of mapped reads = 1,919,576 (99.92%) number of secondary alignments = 721 number of mapped paired reads (first in pair) = 959,862 number of mapped paired reads (second in pair) = 959,714 number of mapped paired reads (both in pair) = 1,917,954 number of mapped paired reads (singletons) = 1,622 number of mapped bases = 164,221,289 bp number of sequenced bases = 164,116,277 bp number of aligned bases = 0 bp number of duplicated reads (flagged) = 86,798 >>>>>>> Insert size mean insert size = 628.3402 std insert size = 14,810.4988 median insert size = 480 >>>>>>> Mapping quality mean mapping quality = 54.629 >>>>>>> ACTG content number of A's = 40,414,310 bp (24.63%) number of C's = 41,798,019 bp (25.47%) number of T's = 40,389,320 bp (24.61%) number of G's = 41,491,642 bp (25.28%) number of N's = 22,986 bp (0.01%) GC percentage = 50.75% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,537,639 number of insertions = 31,672 mapped reads with insertion percentage = 1.61% number of deletions = 36,571 mapped reads with deletion percentage = 1.84% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 19.9781X std coverageData = 11.0986X There is a 90.19% of reference with a coverageData >= 1X There is a 89.11% of reference with a coverageData >= 2X There is a 88.23% of reference with a coverageData >= 3X There is a 87.37% of reference with a coverageData >= 4X There is a 86.51% of reference with a coverageData >= 5X There is a 85.6% of reference with a coverageData >= 6X There is a 84.64% of reference with a coverageData >= 7X There is a 83.59% of reference with a coverageData >= 8X There is a 82.45% of reference with a coverageData >= 9X There is a 81.21% of reference with a coverageData >= 10X There is a 79.84% of reference with a coverageData >= 11X There is a 78.32% of reference with a coverageData >= 12X There is a 76.62% of reference with a coverageData >= 13X There is a 74.7% of reference with a coverageData >= 14X There is a 72.56% of reference with a coverageData >= 15X There is a 70.15% of reference with a coverageData >= 16X There is a 67.44% of reference with a coverageData >= 17X There is a 64.45% of reference with a coverageData >= 18X There is a 61.15% of reference with a coverageData >= 19X There is a 57.57% of reference with a coverageData >= 20X There is a 53.75% of reference with a coverageData >= 21X There is a 49.73% of reference with a coverageData >= 22X There is a 45.55% of reference with a coverageData >= 23X There is a 41.25% of reference with a coverageData >= 24X There is a 37.02% of reference with a coverageData >= 25X There is a 32.83% of reference with a coverageData >= 26X There is a 28.82% of reference with a coverageData >= 27X There is a 24.99% of reference with a coverageData >= 28X There is a 21.4% of reference with a coverageData >= 29X There is a 18.11% of reference with a coverageData >= 30X There is a 15.13% of reference with a coverageData >= 31X There is a 12.49% of reference with a coverageData >= 32X There is a 10.2% of reference with a coverageData >= 33X There is a 8.24% of reference with a coverageData >= 34X There is a 6.6% of reference with a coverageData >= 35X There is a 5.24% of reference with a coverageData >= 36X There is a 4.13% of reference with a coverageData >= 37X There is a 3.23% of reference with a coverageData >= 38X There is a 2.52% of reference with a coverageData >= 39X There is a 1.94% of reference with a coverageData >= 40X There is a 1.5% of reference with a coverageData >= 41X There is a 1.15% of reference with a coverageData >= 42X There is a 0.89% of reference with a coverageData >= 43X There is a 0.7% of reference with a coverageData >= 44X There is a 0.55% of reference with a coverageData >= 45X There is a 0.45% of reference with a coverageData >= 46X There is a 0.37% of reference with a coverageData >= 47X There is a 0.31% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig 25 2906300 42585731 14.652902659739187 12.797067759070755 26 5313770 121635558 22.89063282754052 8.77490891057158