BamQC report ----------------------------------- >>>>>>> Input bam file = ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787973_hisat2.bam outfile = ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787973/genome_results.txt >>>>>>> Reference number of bases = 4,411,532 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 30,696,554 number of mapped reads = 29,624,550 (96.51%) number of mapped paired reads (first in pair) = 14,802,984 number of mapped paired reads (second in pair) = 14,821,566 number of mapped paired reads (both in pair) = 29,408,785 number of mapped paired reads (singletons) = 215,765 number of mapped bases = 115,742,599,173 bp number of sequenced bases = 2,953,496,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,054,757 duplication rate = 68.99% >>>>>>> Insert size mean insert size = 8,821.0127 std insert size = 131,789.52 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 24.3465 >>>>>>> ACTG content number of A's = 541,524,536 bp (18.34%) number of C's = 897,672,803 bp (30.39%) number of T's = 526,554,250 bp (17.83%) number of G's = 987,744,728 bp (33.44%) number of N's = 112,789,006,767 bp (3,818.83%) GC percentage = 63.84% >>>>>>> Mismatches and indels general error rate = 0 number of mismatches = 3,565,057 number of insertions = 16,139 mapped reads with insertion percentage = 0.05% number of deletions = 68,832 mapped reads with deletion percentage = 0.23% homopolymer indels = 60.45% >>>>>>> Coverage mean coverageData = 26,236.373X std coverageData = 36,334.7785X There is a 99.09% of reference with a coverageData >= 1X There is a 98.93% of reference with a coverageData >= 2X There is a 98.74% of reference with a coverageData >= 3X There is a 98.51% of reference with a coverageData >= 4X There is a 98.25% of reference with a coverageData >= 5X There is a 97.98% of reference with a coverageData >= 6X There is a 97.7% of reference with a coverageData >= 7X There is a 97.39% of reference with a coverageData >= 8X There is a 97.07% of reference with a coverageData >= 9X There is a 96.72% of reference with a coverageData >= 10X There is a 96.37% of reference with a coverageData >= 11X There is a 96.03% of reference with a coverageData >= 12X There is a 95.69% of reference with a coverageData >= 13X There is a 95.34% of reference with a coverageData >= 14X There is a 94.98% of reference with a coverageData >= 15X There is a 94.62% of reference with a coverageData >= 16X There is a 94.26% of reference with a coverageData >= 17X There is a 93.9% of reference with a coverageData >= 18X There is a 93.53% of reference with a coverageData >= 19X There is a 93.15% of reference with a coverageData >= 20X There is a 92.77% of reference with a coverageData >= 21X There is a 92.39% of reference with a coverageData >= 22X There is a 92.02% of reference with a coverageData >= 23X There is a 91.64% of reference with a coverageData >= 24X There is a 91.24% of reference with a coverageData >= 25X There is a 90.84% of reference with a coverageData >= 26X There is a 90.44% of reference with a coverageData >= 27X There is a 90.03% of reference with a coverageData >= 28X There is a 89.63% of reference with a coverageData >= 29X There is a 89.23% of reference with a coverageData >= 30X There is a 88.83% of reference with a coverageData >= 31X There is a 88.43% of reference with a coverageData >= 32X There is a 88.03% of reference with a coverageData >= 33X There is a 87.63% of reference with a coverageData >= 34X There is a 87.22% of reference with a coverageData >= 35X There is a 86.83% of reference with a coverageData >= 36X There is a 86.44% of reference with a coverageData >= 37X There is a 86.04% of reference with a coverageData >= 38X There is a 85.65% of reference with a coverageData >= 39X There is a 85.27% of reference with a coverageData >= 40X There is a 84.88% of reference with a coverageData >= 41X There is a 84.5% of reference with a coverageData >= 42X There is a 84.11% of reference with a coverageData >= 43X There is a 83.72% of reference with a coverageData >= 44X There is a 83.33% of reference with a coverageData >= 45X There is a 82.93% of reference with a coverageData >= 46X There is a 82.54% of reference with a coverageData >= 47X There is a 82.15% of reference with a coverageData >= 48X There is a 81.76% of reference with a coverageData >= 49X There is a 81.38% of reference with a coverageData >= 50X There is a 81.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig AL123456.3 4411532 115742599173 26236.373027102603 36334.77845142253