BamQC report
-----------------------------------

>>>>>>> Input

     bam file = x_bam
     outfile = results/genome_results.txt


>>>>>>> Reference

     number of bases = 1,817,261 bp
     number of contigs = 1


>>>>>>> Globals

     number of windows = 400

     number of reads = 1,248,774
     number of mapped reads = 1,242,183 (99.47%)
     number of supplementary alignments = 3,386 (0.27%)
     number of secondary alignments = 0

     number of mapped paired reads (first in pair) = 623,192
     number of mapped paired reads (second in pair) = 618,991
     number of mapped paired reads (both in pair) = 1,237,764
     number of mapped paired reads (singletons) = 4,419
     number of overlapping read pairs = 463,596

     number of mapped bases = 366,875,582 bp
     number of sequenced bases = 366,823,893 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 673,527
     duplication rate = 47.01%


>>>>>>> Insert size

     mean insert size = 1,097.678
     std insert size = 27,365.2401
     median insert size = 524


>>>>>>> Mapping quality

     mean mapping quality = 58.4552


>>>>>>> ACTG content

     number of A's = 109,576,306 bp (29.87%)
     number of C's = 73,524,910 bp (20.04%)
     number of T's = 111,308,231 bp (30.34%)
     number of G's = 72,414,446 bp (19.74%)
     number of N's = 0 bp (0%)

     GC percentage = 39.78%


>>>>>>> Mismatches and indels

    general error rate = 0.0098
    number of mismatches = 3,560,959
    number of insertions = 7,229
    mapped reads with insertion percentage = 0.56%
    number of deletions = 14,669
    mapped reads with deletion percentage = 1.15%
    homopolymer indels = 46.92%


>>>>>>> Coverage

     mean coverageData = 201.8838X
     std coverageData = 112.2733X
     paired-end adapted mean coverage = 177.4988X

     There is a 99.81% of reference with a coverageData >= 1X
     There is a 99.77% of reference with a coverageData >= 2X
     There is a 99.74% of reference with a coverageData >= 3X
     There is a 99.7% of reference with a coverageData >= 4X
     There is a 99.66% of reference with a coverageData >= 5X
     There is a 99.6% of reference with a coverageData >= 6X
     There is a 99.53% of reference with a coverageData >= 7X
     There is a 99.41% of reference with a coverageData >= 8X
     There is a 99.3% of reference with a coverageData >= 9X
     There is a 99.21% of reference with a coverageData >= 10X
     There is a 99.11% of reference with a coverageData >= 11X
     There is a 98.99% of reference with a coverageData >= 12X
     There is a 98.87% of reference with a coverageData >= 13X
     There is a 98.76% of reference with a coverageData >= 14X
     There is a 98.63% of reference with a coverageData >= 15X
     There is a 98.5% of reference with a coverageData >= 16X
     There is a 98.35% of reference with a coverageData >= 17X
     There is a 98.16% of reference with a coverageData >= 18X
     There is a 97.97% of reference with a coverageData >= 19X
     There is a 97.79% of reference with a coverageData >= 20X
     There is a 97.59% of reference with a coverageData >= 21X
     There is a 97.37% of reference with a coverageData >= 22X
     There is a 97.16% of reference with a coverageData >= 23X
     There is a 96.95% of reference with a coverageData >= 24X
     There is a 96.71% of reference with a coverageData >= 25X
     There is a 96.48% of reference with a coverageData >= 26X
     There is a 96.24% of reference with a coverageData >= 27X
     There is a 95.99% of reference with a coverageData >= 28X
     There is a 95.73% of reference with a coverageData >= 29X
     There is a 95.49% of reference with a coverageData >= 30X
     There is a 95.23% of reference with a coverageData >= 31X
     There is a 94.99% of reference with a coverageData >= 32X
     There is a 94.75% of reference with a coverageData >= 33X
     There is a 94.51% of reference with a coverageData >= 34X
     There is a 94.27% of reference with a coverageData >= 35X
     There is a 94.01% of reference with a coverageData >= 36X
     There is a 93.8% of reference with a coverageData >= 37X
     There is a 93.55% of reference with a coverageData >= 38X
     There is a 93.31% of reference with a coverageData >= 39X
     There is a 93.04% of reference with a coverageData >= 40X
     There is a 92.77% of reference with a coverageData >= 41X
     There is a 92.52% of reference with a coverageData >= 42X
     There is a 92.27% of reference with a coverageData >= 43X
     There is a 91.99% of reference with a coverageData >= 44X
     There is a 91.72% of reference with a coverageData >= 45X
     There is a 91.44% of reference with a coverageData >= 46X
     There is a 91.17% of reference with a coverageData >= 47X
     There is a 90.9% of reference with a coverageData >= 48X
     There is a 90.64% of reference with a coverageData >= 49X
     There is a 90.4% of reference with a coverageData >= 50X
     There is a 90.15% of reference with a coverageData >= 51X


>>>>>>> Coverage per contig

	NZ_CP031250.1	1817261	366875582	201.88381415768015	112.27329056357358