BamQC report ----------------------------------- >>>>>>> Input bam file = ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792493_hisat2.bam outfile = ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792493/genome_results.txt >>>>>>> Reference number of bases = 4,411,532 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 29,615,840 number of mapped reads = 28,011,529 (94.58%) number of mapped paired reads (first in pair) = 14,001,270 number of mapped paired reads (second in pair) = 14,010,259 number of mapped paired reads (both in pair) = 27,702,476 number of mapped paired reads (singletons) = 309,053 number of mapped bases = 248,689,231,559 bp number of sequenced bases = 2,789,297,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,655,585 duplication rate = 66.2% >>>>>>> Insert size mean insert size = 15,900.9972 std insert size = 178,012.7115 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 22.3384 >>>>>>> ACTG content number of A's = 535,314,114 bp (19.19%) number of C's = 840,449,512 bp (30.13%) number of T's = 499,893,352 bp (17.92%) number of G's = 913,640,694 bp (32.76%) number of N's = 245,899,817,797 bp (8,815.83%) GC percentage = 62.89% >>>>>>> Mismatches and indels general error rate = 0 number of mismatches = 3,635,014 number of insertions = 11,207 mapped reads with insertion percentage = 0.04% number of deletions = 84,271 mapped reads with deletion percentage = 0.3% homopolymer indels = 50.14% >>>>>>> Coverage mean coverageData = 56,372.5326X std coverageData = 66,421.7922X There is a 98.84% of reference with a coverageData >= 1X There is a 98.52% of reference with a coverageData >= 2X There is a 98.13% of reference with a coverageData >= 3X There is a 97.72% of reference with a coverageData >= 4X There is a 97.3% of reference with a coverageData >= 5X There is a 96.89% of reference with a coverageData >= 6X There is a 96.44% of reference with a coverageData >= 7X There is a 95.99% of reference with a coverageData >= 8X There is a 95.52% of reference with a coverageData >= 9X There is a 95.05% of reference with a coverageData >= 10X There is a 94.6% of reference with a coverageData >= 11X There is a 94.11% of reference with a coverageData >= 12X There is a 93.62% of reference with a coverageData >= 13X There is a 93.11% of reference with a coverageData >= 14X There is a 92.62% of reference with a coverageData >= 15X There is a 92.11% of reference with a coverageData >= 16X There is a 91.61% of reference with a coverageData >= 17X There is a 91.1% of reference with a coverageData >= 18X There is a 90.61% of reference with a coverageData >= 19X There is a 90.12% of reference with a coverageData >= 20X There is a 89.62% of reference with a coverageData >= 21X There is a 89.11% of reference with a coverageData >= 22X There is a 88.62% of reference with a coverageData >= 23X There is a 88.12% of reference with a coverageData >= 24X There is a 87.62% of reference with a coverageData >= 25X There is a 87.11% of reference with a coverageData >= 26X There is a 86.61% of reference with a coverageData >= 27X There is a 86.1% of reference with a coverageData >= 28X There is a 85.6% of reference with a coverageData >= 29X There is a 85.09% of reference with a coverageData >= 30X There is a 84.6% of reference with a coverageData >= 31X There is a 84.08% of reference with a coverageData >= 32X There is a 83.57% of reference with a coverageData >= 33X There is a 83.07% of reference with a coverageData >= 34X There is a 82.57% of reference with a coverageData >= 35X There is a 82.08% of reference with a coverageData >= 36X There is a 81.6% of reference with a coverageData >= 37X There is a 81.13% of reference with a coverageData >= 38X There is a 80.65% of reference with a coverageData >= 39X There is a 80.18% of reference with a coverageData >= 40X There is a 79.72% of reference with a coverageData >= 41X There is a 79.26% of reference with a coverageData >= 42X There is a 78.8% of reference with a coverageData >= 43X There is a 78.35% of reference with a coverageData >= 44X There is a 77.89% of reference with a coverageData >= 45X There is a 77.43% of reference with a coverageData >= 46X There is a 76.98% of reference with a coverageData >= 47X There is a 76.53% of reference with a coverageData >= 48X There is a 76.09% of reference with a coverageData >= 49X There is a 75.65% of reference with a coverageData >= 50X There is a 75.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig AL123456.3 4411532 248689231559 56372.53261656041 66421.7921634617