BamQC report ----------------------------------- >>>>>>> Input bam file = ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25787974_hisat2.bam outfile = ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25787974/genome_results.txt >>>>>>> Reference number of bases = 4,411,532 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 26,007,427 number of mapped reads = 24,973,370 (96.02%) number of mapped paired reads (first in pair) = 12,480,857 number of mapped paired reads (second in pair) = 12,492,513 number of mapped paired reads (both in pair) = 24,640,558 number of mapped paired reads (singletons) = 332,812 number of mapped bases = 201,327,585,707 bp number of sequenced bases = 2,486,874,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,971,571 duplication rate = 59.74% >>>>>>> Insert size mean insert size = 25,281.1207 std insert size = 227,105.9791 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 14.9448 >>>>>>> ACTG content number of A's = 489,766,344 bp (19.69%) number of C's = 725,928,254 bp (29.19%) number of T's = 450,500,911 bp (18.12%) number of G's = 820,678,592 bp (33%) number of N's = 198,840,615,072 bp (7,995.6%) GC percentage = 62.19% >>>>>>> Mismatches and indels general error rate = 0 number of mismatches = 3,371,174 number of insertions = 8,406 mapped reads with insertion percentage = 0.03% number of deletions = 69,895 mapped reads with deletion percentage = 0.28% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 45,636.6599X std coverageData = 58,722.3625X There is a 98.8% of reference with a coverageData >= 1X There is a 98.41% of reference with a coverageData >= 2X There is a 97.92% of reference with a coverageData >= 3X There is a 97.36% of reference with a coverageData >= 4X There is a 96.74% of reference with a coverageData >= 5X There is a 96.08% of reference with a coverageData >= 6X There is a 95.39% of reference with a coverageData >= 7X There is a 94.73% of reference with a coverageData >= 8X There is a 94.05% of reference with a coverageData >= 9X There is a 93.34% of reference with a coverageData >= 10X There is a 92.62% of reference with a coverageData >= 11X There is a 91.87% of reference with a coverageData >= 12X There is a 91.13% of reference with a coverageData >= 13X There is a 90.39% of reference with a coverageData >= 14X There is a 89.63% of reference with a coverageData >= 15X There is a 88.89% of reference with a coverageData >= 16X There is a 88.13% of reference with a coverageData >= 17X There is a 87.37% of reference with a coverageData >= 18X There is a 86.6% of reference with a coverageData >= 19X There is a 85.86% of reference with a coverageData >= 20X There is a 85.13% of reference with a coverageData >= 21X There is a 84.41% of reference with a coverageData >= 22X There is a 83.69% of reference with a coverageData >= 23X There is a 82.97% of reference with a coverageData >= 24X There is a 82.25% of reference with a coverageData >= 25X There is a 81.54% of reference with a coverageData >= 26X There is a 80.81% of reference with a coverageData >= 27X There is a 80.1% of reference with a coverageData >= 28X There is a 79.4% of reference with a coverageData >= 29X There is a 78.7% of reference with a coverageData >= 30X There is a 78.02% of reference with a coverageData >= 31X There is a 77.33% of reference with a coverageData >= 32X There is a 76.65% of reference with a coverageData >= 33X There is a 75.98% of reference with a coverageData >= 34X There is a 75.3% of reference with a coverageData >= 35X There is a 74.63% of reference with a coverageData >= 36X There is a 73.96% of reference with a coverageData >= 37X There is a 73.3% of reference with a coverageData >= 38X There is a 72.65% of reference with a coverageData >= 39X There is a 72% of reference with a coverageData >= 40X There is a 71.37% of reference with a coverageData >= 41X There is a 70.74% of reference with a coverageData >= 42X There is a 70.13% of reference with a coverageData >= 43X There is a 69.53% of reference with a coverageData >= 44X There is a 68.93% of reference with a coverageData >= 45X There is a 68.34% of reference with a coverageData >= 46X There is a 67.76% of reference with a coverageData >= 47X There is a 67.17% of reference with a coverageData >= 48X There is a 66.59% of reference with a coverageData >= 49X There is a 66.02% of reference with a coverageData >= 50X There is a 65.46% of reference with a coverageData >= 51X >>>>>>> Coverage per contig AL123456.3 4411532 201327585707 45636.65994194307 58722.36245447811