BamQC report ----------------------------------- >>>>>>> Input bam file = ../mtuberculosis2/2-alignment/pathogen/bam/mycobacteriumTuberculosis/SRR25792495_hisat2.bam outfile = ../mtuberculosis2/3-qualimap/mycobacteriumTuberculosis/SRR25792495/genome_results.txt >>>>>>> Reference number of bases = 4,411,532 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 34,732,954 number of mapped reads = 29,829,027 (85.88%) number of mapped paired reads (first in pair) = 14,639,335 number of mapped paired reads (second in pair) = 15,189,692 number of mapped paired reads (both in pair) = 29,467,908 number of mapped paired reads (singletons) = 361,119 number of mapped bases = 17,942,784,928 bp number of sequenced bases = 2,943,215,718 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,638,321 duplication rate = 27.61% >>>>>>> Insert size mean insert size = 280.5475 std insert size = 14,783.9454 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 27.7811 >>>>>>> ACTG content number of A's = 686,445,557 bp (23.32%) number of C's = 680,897,137 bp (23.13%) number of T's = 545,705,997 bp (18.54%) number of G's = 1,030,167,027 bp (35%) number of N's = 14,999,477,074 bp (509.63%) GC percentage = 58.14% >>>>>>> Mismatches and indels general error rate = 0.0003 number of mismatches = 4,915,857 number of insertions = 5,563 mapped reads with insertion percentage = 0.02% number of deletions = 83,095 mapped reads with deletion percentage = 0.28% homopolymer indels = 77.36% >>>>>>> Coverage mean coverageData = 4,067.2458X std coverageData = 29,124.1095X There is a 68.88% of reference with a coverageData >= 1X There is a 55.85% of reference with a coverageData >= 2X There is a 43.75% of reference with a coverageData >= 3X There is a 36.29% of reference with a coverageData >= 4X There is a 30.29% of reference with a coverageData >= 5X There is a 26.04% of reference with a coverageData >= 6X There is a 22.61% of reference with a coverageData >= 7X There is a 19.97% of reference with a coverageData >= 8X There is a 17.79% of reference with a coverageData >= 9X There is a 16.07% of reference with a coverageData >= 10X There is a 14.57% of reference with a coverageData >= 11X There is a 13.32% of reference with a coverageData >= 12X There is a 12.22% of reference with a coverageData >= 13X There is a 11.28% of reference with a coverageData >= 14X There is a 10.43% of reference with a coverageData >= 15X There is a 9.69% of reference with a coverageData >= 16X There is a 9.02% of reference with a coverageData >= 17X There is a 8.43% of reference with a coverageData >= 18X There is a 7.88% of reference with a coverageData >= 19X There is a 7.4% of reference with a coverageData >= 20X There is a 6.98% of reference with a coverageData >= 21X There is a 6.61% of reference with a coverageData >= 22X There is a 6.25% of reference with a coverageData >= 23X There is a 5.94% of reference with a coverageData >= 24X There is a 5.64% of reference with a coverageData >= 25X There is a 5.38% of reference with a coverageData >= 26X There is a 5.13% of reference with a coverageData >= 27X There is a 4.89% of reference with a coverageData >= 28X There is a 4.67% of reference with a coverageData >= 29X There is a 4.47% of reference with a coverageData >= 30X There is a 4.29% of reference with a coverageData >= 31X There is a 4.12% of reference with a coverageData >= 32X There is a 3.96% of reference with a coverageData >= 33X There is a 3.82% of reference with a coverageData >= 34X There is a 3.68% of reference with a coverageData >= 35X There is a 3.56% of reference with a coverageData >= 36X There is a 3.43% of reference with a coverageData >= 37X There is a 3.32% of reference with a coverageData >= 38X There is a 3.21% of reference with a coverageData >= 39X There is a 3.11% of reference with a coverageData >= 40X There is a 3.02% of reference with a coverageData >= 41X There is a 2.93% of reference with a coverageData >= 42X There is a 2.84% of reference with a coverageData >= 43X There is a 2.76% of reference with a coverageData >= 44X There is a 2.69% of reference with a coverageData >= 45X There is a 2.61% of reference with a coverageData >= 46X There is a 2.54% of reference with a coverageData >= 47X There is a 2.48% of reference with a coverageData >= 48X There is a 2.41% of reference with a coverageData >= 49X There is a 2.34% of reference with a coverageData >= 50X There is a 2.28% of reference with a coverageData >= 51X >>>>>>> Coverage per contig AL123456.3 4411532 17942784928 4067.245784004287 29124.109459763247