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

>>>>>>> Input

     bam file = SRR389222_sub3_trimmed_bismark_bt2.deduplicated.sorted.bam
     outfile = SRR389222_sub3_trimmed_bismark_bt2.deduplicated_qualimap/genome_results.txt


>>>>>>> Reference

     number of bases = 48,502 bp
     number of contigs = 1


>>>>>>> Globals

     number of windows = 398

     number of reads = 311
     number of mapped reads = 311 (100%)
     number of secondary alignments = 0

     number of mapped bases = 10,964 bp
     number of sequenced bases = 10,962 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 10
     duplication rate = 2.99%


>>>>>>> Insert size

     mean insert size = 0
     std insert size = 0
     median insert size = 0


>>>>>>> Mapping quality

     mean mapping quality = 0.3826


>>>>>>> ACTG content

     number of A's = 2,745 bp (25.04%)
     number of C's = 115 bp (1.05%)
     number of T's = 4,831 bp (44.07%)
     number of G's = 3,271 bp (29.84%)
     number of N's = 2 bp (0.02%)

     GC percentage = 30.89%


>>>>>>> Mismatches and indels

    general error rate = 0.2581
    number of mismatches = 2,830


>>>>>>> Coverage

     mean coverageData = 0.2261X
     std coverageData = 2.7642X

     There is a 0.74% of reference with a coverageData >= 1X
     There is a 0.74% of reference with a coverageData >= 2X
     There is a 0.73% of reference with a coverageData >= 3X
     There is a 0.73% of reference with a coverageData >= 4X
     There is a 0.73% of reference with a coverageData >= 5X
     There is a 0.72% of reference with a coverageData >= 6X
     There is a 0.71% of reference with a coverageData >= 7X
     There is a 0.7% of reference with a coverageData >= 8X
     There is a 0.7% of reference with a coverageData >= 9X
     There is a 0.69% of reference with a coverageData >= 10X
     There is a 0.68% of reference with a coverageData >= 11X
     There is a 0.67% of reference with a coverageData >= 12X
     There is a 0.66% of reference with a coverageData >= 13X
     There is a 0.65% of reference with a coverageData >= 14X
     There is a 0.65% of reference with a coverageData >= 15X
     There is a 0.64% of reference with a coverageData >= 16X
     There is a 0.63% of reference with a coverageData >= 17X
     There is a 0.62% of reference with a coverageData >= 18X
     There is a 0.61% of reference with a coverageData >= 19X
     There is a 0.6% of reference with a coverageData >= 20X
     There is a 0.59% of reference with a coverageData >= 21X
     There is a 0.59% of reference with a coverageData >= 22X
     There is a 0.58% of reference with a coverageData >= 23X
     There is a 0.58% of reference with a coverageData >= 24X
     There is a 0.57% of reference with a coverageData >= 25X
     There is a 0.55% of reference with a coverageData >= 26X
     There is a 0.55% of reference with a coverageData >= 27X
     There is a 0.54% of reference with a coverageData >= 28X
     There is a 0.53% of reference with a coverageData >= 29X
     There is a 0.53% of reference with a coverageData >= 30X
     There is a 0.52% of reference with a coverageData >= 31X
     There is a 0.51% of reference with a coverageData >= 32X
     There is a 0.5% of reference with a coverageData >= 33X
     There is a 0.48% of reference with a coverageData >= 34X
     There is a 0.44% of reference with a coverageData >= 35X
     There is a 0.34% of reference with a coverageData >= 36X
     There is a 0.17% of reference with a coverageData >= 37X
     There is a 0.12% of reference with a coverageData >= 38X
     There is a 0.09% of reference with a coverageData >= 39X
     There is a 0.08% of reference with a coverageData >= 40X
     There is a 0.05% of reference with a coverageData >= 41X
     There is a 0.04% of reference with a coverageData >= 42X
     There is a 0.02% of reference with a coverageData >= 43X
     There is a 0% of reference with a coverageData >= 44X
     There is a 0% of reference with a coverageData >= 45X
     There is a 0% of reference with a coverageData >= 46X
     There is a 0% of reference with a coverageData >= 47X
     There is a 0% of reference with a coverageData >= 48X
     There is a 0% of reference with a coverageData >= 49X
     There is a 0% of reference with a coverageData >= 50X
     There is a 0% of reference with a coverageData >= 51X


>>>>>>> Coverage per contig

	chr	48502	10964	0.22605253391612717	2.764178753749228