BamQC report ----------------------------------- >>>>>>> Input bam file = ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787975_hisat2.bam outfile = ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787975/genome_results.txt >>>>>>> Reference number of bases = 4,411,532 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 32,347,422 number of mapped reads = 30,540,696 (94.41%) number of mapped paired reads (first in pair) = 15,053,461 number of mapped paired reads (second in pair) = 15,487,235 number of mapped paired reads (both in pair) = 30,179,767 number of mapped paired reads (singletons) = 360,929 number of mapped bases = 56,222,600,368 bp number of sequenced bases = 3,028,919,870 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,579,016 duplication rate = 42.6% >>>>>>> Insert size mean insert size = 4,852.43 std insert size = 98,947.7562 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 26.1173 >>>>>>> ACTG content number of A's = 665,947,440 bp (21.99%) number of C's = 774,121,281 bp (25.56%) number of T's = 587,669,493 bp (19.4%) number of G's = 1,001,181,656 bp (33.05%) number of N's = 53,193,601,872 bp (1,756.19%) GC percentage = 58.61% >>>>>>> Mismatches and indels general error rate = 0.0001 number of mismatches = 3,601,348 number of insertions = 4,754 mapped reads with insertion percentage = 0.02% number of deletions = 57,171 mapped reads with deletion percentage = 0.19% homopolymer indels = 56.8% >>>>>>> Coverage mean coverageData = 12,744.4616X std coverageData = 29,737.1205X There is a 98.13% of reference with a coverageData >= 1X There is a 96.52% of reference with a coverageData >= 2X There is a 94.27% of reference with a coverageData >= 3X There is a 91.66% of reference with a coverageData >= 4X There is a 88.81% of reference with a coverageData >= 5X There is a 85.87% of reference with a coverageData >= 6X There is a 82.91% of reference with a coverageData >= 7X There is a 80.05% of reference with a coverageData >= 8X There is a 77.24% of reference with a coverageData >= 9X There is a 74.5% of reference with a coverageData >= 10X There is a 71.87% of reference with a coverageData >= 11X There is a 69.38% of reference with a coverageData >= 12X There is a 66.97% of reference with a coverageData >= 13X There is a 64.71% of reference with a coverageData >= 14X There is a 62.58% of reference with a coverageData >= 15X There is a 60.54% of reference with a coverageData >= 16X There is a 58.63% of reference with a coverageData >= 17X There is a 56.81% of reference with a coverageData >= 18X There is a 55.08% of reference with a coverageData >= 19X There is a 53.41% of reference with a coverageData >= 20X There is a 51.81% of reference with a coverageData >= 21X There is a 50.31% of reference with a coverageData >= 22X There is a 48.86% of reference with a coverageData >= 23X There is a 47.5% of reference with a coverageData >= 24X There is a 46.2% of reference with a coverageData >= 25X There is a 44.99% of reference with a coverageData >= 26X There is a 43.8% of reference with a coverageData >= 27X There is a 42.65% of reference with a coverageData >= 28X There is a 41.55% of reference with a coverageData >= 29X There is a 40.52% of reference with a coverageData >= 30X There is a 39.53% of reference with a coverageData >= 31X There is a 38.58% of reference with a coverageData >= 32X There is a 37.67% of reference with a coverageData >= 33X There is a 36.79% of reference with a coverageData >= 34X There is a 35.92% of reference with a coverageData >= 35X There is a 35.1% of reference with a coverageData >= 36X There is a 34.32% of reference with a coverageData >= 37X There is a 33.55% of reference with a coverageData >= 38X There is a 32.81% of reference with a coverageData >= 39X There is a 32.1% of reference with a coverageData >= 40X There is a 31.42% of reference with a coverageData >= 41X There is a 30.78% of reference with a coverageData >= 42X There is a 30.15% of reference with a coverageData >= 43X There is a 29.55% of reference with a coverageData >= 44X There is a 28.97% of reference with a coverageData >= 45X There is a 28.42% of reference with a coverageData >= 46X There is a 27.89% of reference with a coverageData >= 47X There is a 27.35% of reference with a coverageData >= 48X There is a 26.83% of reference with a coverageData >= 49X There is a 26.33% of reference with a coverageData >= 50X There is a 25.85% of reference with a coverageData >= 51X >>>>>>> Coverage per contig AL123456.3 4411532 56222600368 12744.461644616882 29737.1205206974