BamQC report ----------------------------------- >>>>>>> Input bam file = E2348-69.bam outfile = E2348-69/genome_results.txt >>>>>>> Reference number of bases = 4,848,621 bp number of contigs = 1 >>>>>>> Globals number of windows = 400 number of reads = 5,827,464 number of mapped reads = 5,534,444 (94.97%) number of supplementary alignments = 14,114 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,780,723 number of mapped paired reads (second in pair) = 2,753,721 number of mapped paired reads (both in pair) = 5,500,026 number of mapped paired reads (singletons) = 34,418 number of mapped bases = 750,828,167 bp number of sequenced bases = 750,817,339 bp number of aligned bases = 0 bp number of duplicated reads (flagged) = 191,153 >>>>>>> Insert size mean insert size = 13,126.9609 std insert size = 176,657.3622 median insert size = 365 >>>>>>> Mapping quality mean mapping quality = 58.4911 >>>>>>> ACTG content number of A's = 186,537,405 bp (24.84%) number of C's = 189,585,353 bp (25.25%) number of T's = 185,668,010 bp (24.73%) number of G's = 189,012,413 bp (25.17%) number of N's = 14,158 bp (0%) GC percentage = 50.42% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 1,218,318 number of insertions = 2,213 mapped reads with insertion percentage = 0.04% number of deletions = 6,690 mapped reads with deletion percentage = 0.12% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 154.854X std coverageData = 25.6678X There is a 99.66% of reference with a coverageData >= 1X There is a 99.66% of reference with a coverageData >= 2X There is a 99.66% of reference with a coverageData >= 3X There is a 99.66% of reference with a coverageData >= 4X There is a 99.66% of reference with a coverageData >= 5X There is a 99.66% of reference with a coverageData >= 6X There is a 99.66% of reference with a coverageData >= 7X There is a 99.66% of reference with a coverageData >= 8X There is a 99.66% of reference with a coverageData >= 9X There is a 99.66% of reference with a coverageData >= 10X There is a 99.66% of reference with a coverageData >= 11X There is a 99.66% of reference with a coverageData >= 12X There is a 99.65% of reference with a coverageData >= 13X There is a 99.65% of reference with a coverageData >= 14X There is a 99.65% of reference with a coverageData >= 15X There is a 99.65% of reference with a coverageData >= 16X There is a 99.65% of reference with a coverageData >= 17X There is a 99.65% of reference with a coverageData >= 18X There is a 99.65% of reference with a coverageData >= 19X There is a 99.65% of reference with a coverageData >= 20X There is a 99.65% of reference with a coverageData >= 21X There is a 99.65% of reference with a coverageData >= 22X There is a 99.65% of reference with a coverageData >= 23X There is a 99.65% of reference with a coverageData >= 24X There is a 99.65% of reference with a coverageData >= 25X There is a 99.65% of reference with a coverageData >= 26X There is a 99.65% of reference with a coverageData >= 27X There is a 99.65% of reference with a coverageData >= 28X There is a 99.65% of reference with a coverageData >= 29X There is a 99.64% of reference with a coverageData >= 30X There is a 99.64% of reference with a coverageData >= 31X There is a 99.64% of reference with a coverageData >= 32X There is a 99.64% of reference with a coverageData >= 33X There is a 99.64% of reference with a coverageData >= 34X There is a 99.64% of reference with a coverageData >= 35X There is a 99.64% of reference with a coverageData >= 36X There is a 99.64% of reference with a coverageData >= 37X There is a 99.64% of reference with a coverageData >= 38X There is a 99.64% of reference with a coverageData >= 39X There is a 99.64% of reference with a coverageData >= 40X There is a 99.64% of reference with a coverageData >= 41X There is a 99.63% of reference with a coverageData >= 42X There is a 99.63% of reference with a coverageData >= 43X There is a 99.63% of reference with a coverageData >= 44X There is a 99.63% of reference with a coverageData >= 45X There is a 99.63% of reference with a coverageData >= 46X There is a 99.63% of reference with a coverageData >= 47X There is a 99.63% of reference with a coverageData >= 48X There is a 99.63% of reference with a coverageData >= 49X There is a 99.63% of reference with a coverageData >= 50X There is a 99.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig 1 4848621 750828167 154.85396095095905 25.667812972682885