BamQC report ----------------------------------- >>>>>>> Input bam file = ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787976_hisat2.bam outfile = ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787976/genome_results.txt >>>>>>> Reference number of bases = 4,411,532 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 33,341,480 number of mapped reads = 32,302,443 (96.88%) number of mapped paired reads (first in pair) = 16,162,819 number of mapped paired reads (second in pair) = 16,139,624 number of mapped paired reads (both in pair) = 32,027,228 number of mapped paired reads (singletons) = 275,215 number of mapped bases = 183,227,181,772 bp number of sequenced bases = 3,220,115,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,043,140 duplication rate = 63.86% >>>>>>> Insert size mean insert size = 10,824.1812 std insert size = 146,498.5175 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 23.4399 >>>>>>> ACTG content number of A's = 630,135,338 bp (19.57%) number of C's = 946,950,944 bp (29.41%) number of T's = 583,281,943 bp (18.11%) number of G's = 1,059,747,664 bp (32.91%) number of N's = 180,006,970,651 bp (5,590.08%) GC percentage = 62.32% >>>>>>> Mismatches and indels general error rate = 0 number of mismatches = 3,546,495 number of insertions = 8,380 mapped reads with insertion percentage = 0.03% number of deletions = 69,331 mapped reads with deletion percentage = 0.21% homopolymer indels = 55.34% >>>>>>> Coverage mean coverageData = 41,533.6853X std coverageData = 64,951.3363X There is a 99.18% of reference with a coverageData >= 1X There is a 98.94% of reference with a coverageData >= 2X There is a 98.63% of reference with a coverageData >= 3X There is a 98.27% of reference with a coverageData >= 4X There is a 97.9% of reference with a coverageData >= 5X There is a 97.48% of reference with a coverageData >= 6X There is a 97.02% of reference with a coverageData >= 7X There is a 96.54% of reference with a coverageData >= 8X There is a 96.07% of reference with a coverageData >= 9X There is a 95.58% of reference with a coverageData >= 10X There is a 95.1% of reference with a coverageData >= 11X There is a 94.59% of reference with a coverageData >= 12X There is a 94.09% of reference with a coverageData >= 13X There is a 93.6% of reference with a coverageData >= 14X There is a 93.1% of reference with a coverageData >= 15X There is a 92.57% of reference with a coverageData >= 16X There is a 92.04% of reference with a coverageData >= 17X There is a 91.5% of reference with a coverageData >= 18X There is a 90.97% of reference with a coverageData >= 19X There is a 90.43% of reference with a coverageData >= 20X There is a 89.87% of reference with a coverageData >= 21X There is a 89.33% of reference with a coverageData >= 22X There is a 88.78% of reference with a coverageData >= 23X There is a 88.22% of reference with a coverageData >= 24X There is a 87.67% of reference with a coverageData >= 25X There is a 87.11% of reference with a coverageData >= 26X There is a 86.55% of reference with a coverageData >= 27X There is a 86% of reference with a coverageData >= 28X There is a 85.44% of reference with a coverageData >= 29X There is a 84.89% of reference with a coverageData >= 30X There is a 84.34% of reference with a coverageData >= 31X There is a 83.81% of reference with a coverageData >= 32X There is a 83.27% of reference with a coverageData >= 33X There is a 82.73% of reference with a coverageData >= 34X There is a 82.21% of reference with a coverageData >= 35X There is a 81.69% of reference with a coverageData >= 36X There is a 81.17% of reference with a coverageData >= 37X There is a 80.64% of reference with a coverageData >= 38X There is a 80.12% of reference with a coverageData >= 39X There is a 79.59% of reference with a coverageData >= 40X There is a 79.08% of reference with a coverageData >= 41X There is a 78.56% of reference with a coverageData >= 42X There is a 78.04% of reference with a coverageData >= 43X There is a 77.53% of reference with a coverageData >= 44X There is a 77.02% of reference with a coverageData >= 45X There is a 76.53% of reference with a coverageData >= 46X There is a 76.04% of reference with a coverageData >= 47X There is a 75.55% of reference with a coverageData >= 48X There is a 75.05% of reference with a coverageData >= 49X There is a 74.57% of reference with a coverageData >= 50X There is a 74.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig AL123456.3 4411532 183227181772 41533.68529844054 64951.336313596745