annotate test-data/genome_results_default.txt @ 2:43a1c3e1a4d0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 3c0443b29b1fac5ec193912b0c03a79d75ba731a"

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

>>>>>>> Input

     bam file = /tmp/tmprT4oZK/files/b/1/f/dataset_b1fbaad4-1b5a-4769-8a15-b4cec4de5731.dat
     outfile = results/genome_results.txt


>>>>>>> Reference

     number of bases = 650 bp
     number of contigs = 1


>>>>>>> Globals

     number of windows = 325

     number of reads = 100
     number of mapped reads = 100 (100%)
     number of secondary alignments = 1

     number of mapped bases = 12,665 bp
     number of sequenced bases = 7,465 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 18
     duplication rate = 15.85%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 115.8402


>>>>>>> ACTG content

     number of A's = 1,910 bp (25.59%)
     number of C's = 1,902 bp (25.48%)
     number of T's = 1,497 bp (20.05%)
     number of G's = 2,156 bp (28.88%)
     number of N's = 0 bp (0%)

     GC percentage = 54.36%


>>>>>>> Mismatches and indels

    general error rate = 0.0118
    number of mismatches = 149


>>>>>>> Coverage

     mean coverageData = 19.4846X
     std coverageData = 16.5813X

     There is a 45.85% of reference with a coverageData >= 1X
     There is a 45.38% of reference with a coverageData >= 2X
     There is a 44.92% of reference with a coverageData >= 3X
     There is a 44.62% of reference with a coverageData >= 4X
     There is a 43.85% of reference with a coverageData >= 5X
     There is a 41.85% of reference with a coverageData >= 6X
     There is a 40.46% of reference with a coverageData >= 7X
     There is a 39.85% of reference with a coverageData >= 8X
     There is a 38.77% of reference with a coverageData >= 9X
     There is a 38% of reference with a coverageData >= 10X
     There is a 37.23% of reference with a coverageData >= 11X
     There is a 36.92% of reference with a coverageData >= 12X
     There is a 36.46% of reference with a coverageData >= 13X
     There is a 36.15% of reference with a coverageData >= 14X
     There is a 35.54% of reference with a coverageData >= 15X
     There is a 35.23% of reference with a coverageData >= 16X
     There is a 34.77% of reference with a coverageData >= 17X
     There is a 34% of reference with a coverageData >= 18X
     There is a 33.38% of reference with a coverageData >= 19X
     There is a 33.38% of reference with a coverageData >= 20X
     There is a 33.23% of reference with a coverageData >= 21X
     There is a 31.85% of reference with a coverageData >= 22X
     There is a 31.54% of reference with a coverageData >= 23X
     There is a 30.92% of reference with a coverageData >= 24X
     There is a 30.62% of reference with a coverageData >= 25X
     There is a 28.62% of reference with a coverageData >= 26X
     There is a 27.54% of reference with a coverageData >= 27X
     There is a 26.92% of reference with a coverageData >= 28X
     There is a 25.23% of reference with a coverageData >= 29X
     There is a 23.38% of reference with a coverageData >= 30X
     There is a 20.77% of reference with a coverageData >= 31X
     There is a 16.77% of reference with a coverageData >= 32X
     There is a 12.15% of reference with a coverageData >= 33X
     There is a 10.15% of reference with a coverageData >= 34X
     There is a 8.62% of reference with a coverageData >= 35X
     There is a 7.38% of reference with a coverageData >= 36X
     There is a 4% of reference with a coverageData >= 37X
     There is a 1.85% of reference with a coverageData >= 38X
     There is a 0.31% of reference with a coverageData >= 39X
     There is a 0% of reference with a coverageData >= 40X
     There is a 0% of reference with a coverageData >= 41X
     There is a 0% of reference with a coverageData >= 42X
     There is a 0% 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

	test_chromosome	650	12665	19.484615384615385	16.581284452141826