BamQC report ----------------------------------- >>>>>>> Input bam file = ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792492_hisat2.bam outfile = ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792492/genome_results.txt >>>>>>> Reference number of bases = 4,411,532 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 33,108,733 number of mapped reads = 32,303,131 (97.57%) number of mapped paired reads (first in pair) = 16,175,687 number of mapped paired reads (second in pair) = 16,127,444 number of mapped paired reads (both in pair) = 32,010,043 number of mapped paired reads (singletons) = 293,088 number of mapped bases = 148,377,689,834 bp number of sequenced bases = 3,222,524,206 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,839,540 duplication rate = 67.22% >>>>>>> Insert size mean insert size = 12,383.4201 std insert size = 159,883.3859 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 20.3541 >>>>>>> ACTG content number of A's = 606,388,620 bp (18.82%) number of C's = 960,447,272 bp (29.8%) number of T's = 581,448,261 bp (18.04%) number of G's = 1,074,240,053 bp (33.34%) number of N's = 145,155,043,069 bp (4,504.39%) GC percentage = 63.14% >>>>>>> Mismatches and indels general error rate = 0 number of mismatches = 4,385,814 number of insertions = 15,441 mapped reads with insertion percentage = 0.05% number of deletions = 90,396 mapped reads with deletion percentage = 0.28% homopolymer indels = 55.78% >>>>>>> Coverage mean coverageData = 33,634.0504X std coverageData = 49,185.0032X There is a 98.96% of reference with a coverageData >= 1X There is a 98.78% of reference with a coverageData >= 2X There is a 98.53% of reference with a coverageData >= 3X There is a 98.29% of reference with a coverageData >= 4X There is a 97.99% of reference with a coverageData >= 5X There is a 97.67% of reference with a coverageData >= 6X There is a 97.33% of reference with a coverageData >= 7X There is a 96.97% of reference with a coverageData >= 8X There is a 96.61% of reference with a coverageData >= 9X There is a 96.25% of reference with a coverageData >= 10X There is a 95.88% of reference with a coverageData >= 11X There is a 95.49% of reference with a coverageData >= 12X There is a 95.1% of reference with a coverageData >= 13X There is a 94.7% of reference with a coverageData >= 14X There is a 94.29% of reference with a coverageData >= 15X There is a 93.89% of reference with a coverageData >= 16X There is a 93.48% of reference with a coverageData >= 17X There is a 93.04% of reference with a coverageData >= 18X There is a 92.62% of reference with a coverageData >= 19X There is a 92.2% of reference with a coverageData >= 20X There is a 91.79% of reference with a coverageData >= 21X There is a 91.37% of reference with a coverageData >= 22X There is a 90.95% of reference with a coverageData >= 23X There is a 90.52% of reference with a coverageData >= 24X There is a 90.09% of reference with a coverageData >= 25X There is a 89.66% of reference with a coverageData >= 26X There is a 89.23% of reference with a coverageData >= 27X There is a 88.8% of reference with a coverageData >= 28X There is a 88.36% of reference with a coverageData >= 29X There is a 87.92% of reference with a coverageData >= 30X There is a 87.48% of reference with a coverageData >= 31X There is a 87.04% of reference with a coverageData >= 32X There is a 86.6% of reference with a coverageData >= 33X There is a 86.15% of reference with a coverageData >= 34X There is a 85.71% of reference with a coverageData >= 35X There is a 85.27% of reference with a coverageData >= 36X There is a 84.84% of reference with a coverageData >= 37X There is a 84.4% of reference with a coverageData >= 38X There is a 83.96% of reference with a coverageData >= 39X There is a 83.53% of reference with a coverageData >= 40X There is a 83.1% of reference with a coverageData >= 41X There is a 82.66% of reference with a coverageData >= 42X There is a 82.22% of reference with a coverageData >= 43X There is a 81.79% of reference with a coverageData >= 44X There is a 81.37% of reference with a coverageData >= 45X There is a 80.94% of reference with a coverageData >= 46X There is a 80.52% of reference with a coverageData >= 47X There is a 80.09% of reference with a coverageData >= 48X There is a 79.67% of reference with a coverageData >= 49X There is a 79.27% of reference with a coverageData >= 50X There is a 78.86% of reference with a coverageData >= 51X >>>>>>> Coverage per contig AL123456.3 4411532 148377689834 33634.05044642088 49185.00316852302