BamQC report ----------------------------------- >>>>>>> Input bam file = ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792494_hisat2.bam outfile = ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792494/genome_results.txt >>>>>>> Reference number of bases = 4,411,532 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 28,007,727 number of mapped reads = 26,959,710 (96.26%) number of mapped paired reads (first in pair) = 13,471,946 number of mapped paired reads (second in pair) = 13,487,764 number of mapped paired reads (both in pair) = 26,759,367 number of mapped paired reads (singletons) = 200,343 number of mapped bases = 167,864,829,252 bp number of sequenced bases = 2,687,481,260 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,463,031 duplication rate = 68.44% >>>>>>> Insert size mean insert size = 7,005.6687 std insert size = 114,258.5624 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 26.7197 >>>>>>> ACTG content number of A's = 487,939,747 bp (18.16%) number of C's = 821,152,857 bp (30.55%) number of T's = 478,401,027 bp (17.8%) number of G's = 899,987,629 bp (33.49%) number of N's = 165,177,243,264 bp (6,146.17%) GC percentage = 64.04% >>>>>>> Mismatches and indels general error rate = 0 number of mismatches = 3,575,158 number of insertions = 11,232 mapped reads with insertion percentage = 0.04% number of deletions = 73,750 mapped reads with deletion percentage = 0.27% homopolymer indels = 54.35% >>>>>>> Coverage mean coverageData = 38,051.3684X std coverageData = 43,773.384X There is a 99.04% of reference with a coverageData >= 1X There is a 98.83% of reference with a coverageData >= 2X There is a 98.55% of reference with a coverageData >= 3X There is a 98.2% of reference with a coverageData >= 4X There is a 97.86% of reference with a coverageData >= 5X There is a 97.47% of reference with a coverageData >= 6X There is a 97.06% of reference with a coverageData >= 7X There is a 96.65% of reference with a coverageData >= 8X There is a 96.24% of reference with a coverageData >= 9X There is a 95.83% of reference with a coverageData >= 10X There is a 95.4% of reference with a coverageData >= 11X There is a 94.99% of reference with a coverageData >= 12X There is a 94.58% of reference with a coverageData >= 13X There is a 94.17% of reference with a coverageData >= 14X There is a 93.75% of reference with a coverageData >= 15X There is a 93.34% of reference with a coverageData >= 16X There is a 92.92% of reference with a coverageData >= 17X There is a 92.49% of reference with a coverageData >= 18X There is a 92.05% of reference with a coverageData >= 19X There is a 91.61% of reference with a coverageData >= 20X There is a 91.18% of reference with a coverageData >= 21X There is a 90.75% of reference with a coverageData >= 22X There is a 90.32% of reference with a coverageData >= 23X There is a 89.89% of reference with a coverageData >= 24X There is a 89.45% of reference with a coverageData >= 25X There is a 89.04% of reference with a coverageData >= 26X There is a 88.63% of reference with a coverageData >= 27X There is a 88.21% of reference with a coverageData >= 28X There is a 87.79% of reference with a coverageData >= 29X There is a 87.37% of reference with a coverageData >= 30X There is a 86.95% of reference with a coverageData >= 31X There is a 86.53% of reference with a coverageData >= 32X There is a 86.11% of reference with a coverageData >= 33X There is a 85.7% of reference with a coverageData >= 34X There is a 85.28% of reference with a coverageData >= 35X There is a 84.86% of reference with a coverageData >= 36X There is a 84.45% of reference with a coverageData >= 37X There is a 84.04% of reference with a coverageData >= 38X There is a 83.61% of reference with a coverageData >= 39X There is a 83.19% of reference with a coverageData >= 40X There is a 82.8% of reference with a coverageData >= 41X There is a 82.39% of reference with a coverageData >= 42X There is a 81.98% of reference with a coverageData >= 43X There is a 81.57% of reference with a coverageData >= 44X There is a 81.16% of reference with a coverageData >= 45X There is a 80.76% of reference with a coverageData >= 46X There is a 80.35% of reference with a coverageData >= 47X There is a 79.95% of reference with a coverageData >= 48X There is a 79.54% of reference with a coverageData >= 49X There is a 79.15% of reference with a coverageData >= 50X There is a 78.75% of reference with a coverageData >= 51X >>>>>>> Coverage per contig AL123456.3 4411532 167864829252 38051.36837996415 43773.384021979015