BamQC report ----------------------------------- >>>>>>> Input bam file = ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787977_hisat2.bam outfile = ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787977/genome_results.txt >>>>>>> Reference number of bases = 4,411,532 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 26,662,258 number of mapped reads = 25,652,129 (96.21%) number of mapped paired reads (first in pair) = 12,829,276 number of mapped paired reads (second in pair) = 12,822,853 number of mapped paired reads (both in pair) = 25,379,585 number of mapped paired reads (singletons) = 272,544 number of mapped bases = 255,905,065,705 bp number of sequenced bases = 2,552,802,188 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,335,611 duplication rate = 65.5% >>>>>>> Insert size mean insert size = 26,929.4358 std insert size = 238,024.6676 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 14.8735 >>>>>>> ACTG content number of A's = 477,884,566 bp (18.72%) number of C's = 772,947,140 bp (30.28%) number of T's = 452,978,233 bp (17.74%) number of G's = 848,992,249 bp (33.26%) number of N's = 253,351,961,114 bp (9,924.47%) GC percentage = 63.54% >>>>>>> Mismatches and indels general error rate = 0 number of mismatches = 5,442,455 number of insertions = 10,843 mapped reads with insertion percentage = 0.04% number of deletions = 238,863 mapped reads with deletion percentage = 0.93% homopolymer indels = 40.33% >>>>>>> Coverage mean coverageData = 58,008.208X std coverageData = 62,454.0823X There is a 99.07% of reference with a coverageData >= 1X There is a 98.84% of reference with a coverageData >= 2X There is a 98.55% of reference with a coverageData >= 3X There is a 98.16% of reference with a coverageData >= 4X There is a 97.72% of reference with a coverageData >= 5X There is a 97.26% of reference with a coverageData >= 6X There is a 96.76% of reference with a coverageData >= 7X There is a 96.24% of reference with a coverageData >= 8X There is a 95.7% of reference with a coverageData >= 9X There is a 95.15% of reference with a coverageData >= 10X There is a 94.59% of reference with a coverageData >= 11X There is a 94.01% of reference with a coverageData >= 12X There is a 93.43% of reference with a coverageData >= 13X There is a 92.83% of reference with a coverageData >= 14X There is a 92.24% of reference with a coverageData >= 15X There is a 91.66% of reference with a coverageData >= 16X There is a 91.07% of reference with a coverageData >= 17X There is a 90.48% of reference with a coverageData >= 18X There is a 89.88% of reference with a coverageData >= 19X There is a 89.28% of reference with a coverageData >= 20X There is a 88.65% of reference with a coverageData >= 21X There is a 88.05% of reference with a coverageData >= 22X There is a 87.44% of reference with a coverageData >= 23X There is a 86.83% of reference with a coverageData >= 24X There is a 86.22% of reference with a coverageData >= 25X There is a 85.61% of reference with a coverageData >= 26X There is a 85% of reference with a coverageData >= 27X There is a 84.41% of reference with a coverageData >= 28X There is a 83.82% of reference with a coverageData >= 29X There is a 83.25% of reference with a coverageData >= 30X There is a 82.69% of reference with a coverageData >= 31X There is a 82.12% of reference with a coverageData >= 32X There is a 81.56% of reference with a coverageData >= 33X There is a 81.02% of reference with a coverageData >= 34X There is a 80.48% of reference with a coverageData >= 35X There is a 79.94% of reference with a coverageData >= 36X There is a 79.41% of reference with a coverageData >= 37X There is a 78.88% of reference with a coverageData >= 38X There is a 78.36% of reference with a coverageData >= 39X There is a 77.84% of reference with a coverageData >= 40X There is a 77.33% of reference with a coverageData >= 41X There is a 76.82% of reference with a coverageData >= 42X There is a 76.33% of reference with a coverageData >= 43X There is a 75.83% of reference with a coverageData >= 44X There is a 75.34% of reference with a coverageData >= 45X There is a 74.83% of reference with a coverageData >= 46X There is a 74.34% of reference with a coverageData >= 47X There is a 73.85% of reference with a coverageData >= 48X There is a 73.37% of reference with a coverageData >= 49X There is a 72.88% of reference with a coverageData >= 50X There is a 72.4% of reference with a coverageData >= 51X >>>>>>> Coverage per contig AL123456.3 4411532 255905065705 58008.20796607618 62454.08231054573