annotate test-data/genome_results_inside_features.txt @ 0:e020be4f281b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"

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

>>>>>>> Input

     bam file = /tmp/tmpB4Sf0A/files/e/d/7/dataset_ed7510d4-c8f3-41fc-8cc1-3b854d9bdf14.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 = 6,451 bp
     number of sequenced bases = 5,101 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 14
     duplication rate = 16.18%


>>>>>>> Globals inside

     regions size = 300 (46.15%)
     number of mapped reads = 82 (82%)


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 251.3687


>>>>>>> ACTG content

     number of A's = 1,243 bp (24.37%)
     number of C's = 1,257 bp (24.64%)
     number of T's = 985 bp (19.31%)
     number of G's = 1,616 bp (31.68%)
     number of N's = 0 bp (0%)

     GC percentage = 56.32%


>>>>>>> Mismatches and indels

    general error rate = 0.0211
    number of mismatches = 136


>>>>>>> Coverage

     mean coverageData = 21.5033X
     std coverageData = 15.658X

     There is a 66% of reference with a coverageData >= 1X
     There is a 65.33% of reference with a coverageData >= 2X
     There is a 65% of reference with a coverageData >= 3X
     There is a 64.33% of reference with a coverageData >= 4X
     There is a 63.33% of reference with a coverageData >= 5X
     There is a 59.67% of reference with a coverageData >= 6X
     There is a 57.67% of reference with a coverageData >= 7X
     There is a 57.67% of reference with a coverageData >= 8X
     There is a 56% of reference with a coverageData >= 9X
     There is a 55% of reference with a coverageData >= 10X
     There is a 54.33% of reference with a coverageData >= 11X
     There is a 54% of reference with a coverageData >= 12X
     There is a 53.33% of reference with a coverageData >= 13X
     There is a 53% of reference with a coverageData >= 14X
     There is a 52.33% of reference with a coverageData >= 15X
     There is a 52.33% of reference with a coverageData >= 16X
     There is a 51.67% of reference with a coverageData >= 17X
     There is a 51% of reference with a coverageData >= 18X
     There is a 50% of reference with a coverageData >= 19X
     There is a 50% of reference with a coverageData >= 20X
     There is a 50% of reference with a coverageData >= 21X
     There is a 49.67% of reference with a coverageData >= 22X
     There is a 49.33% of reference with a coverageData >= 23X
     There is a 48.33% of reference with a coverageData >= 24X
     There is a 48% of reference with a coverageData >= 25X
     There is a 45.33% of reference with a coverageData >= 26X
     There is a 43% of reference with a coverageData >= 27X
     There is a 42% of reference with a coverageData >= 28X
     There is a 39.33% of reference with a coverageData >= 29X
     There is a 35.67% of reference with a coverageData >= 30X
     There is a 32.33% of reference with a coverageData >= 31X
     There is a 25.67% of reference with a coverageData >= 32X
     There is a 16.67% of reference with a coverageData >= 33X
     There is a 13% of reference with a coverageData >= 34X
     There is a 11.33% of reference with a coverageData >= 35X
     There is a 10% of reference with a coverageData >= 36X
     There is a 5.67% of reference with a coverageData >= 37X
     There is a 3% of reference with a coverageData >= 38X
     There is a 0% 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	300	6451	21.503333333333334	15.658011438947867