annotate test-data/genome_results_outside_features.txt @ 2:e7fd6754d093 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/6/4/1/dataset_6416c0ca-3ecd-4273-ae01-22f2ac60965d.dat
     outfile = results/outside_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 = 6,214 bp
     number of sequenced bases = 2,364 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 4
     duplication rate = 14.29%


>>>>>>> Globals outside

     regions size = 350 (53.85%)
     number of mapped reads = 18 (18%)


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 255


>>>>>>> ACTG content

     number of A's = 667 bp (28.21%)
     number of C's = 645 bp (27.28%)
     number of T's = 512 bp (21.66%)
     number of G's = 540 bp (22.84%)
     number of N's = 0 bp (0%)

     GC percentage = 50.13%


>>>>>>> Mismatches and indels

    general error rate = 0.0021
    number of mismatches = 13


>>>>>>> Coverage

     mean coverageData = 17.7543X
     std coverageData = 16.4764X

     There is a 10.58% of reference with a coverageData >= 1X
     There is a 10.58% of reference with a coverageData >= 2X
     There is a 10.58% of reference with a coverageData >= 3X
     There is a 10.58% of reference with a coverageData >= 4X
     There is a 10.58% of reference with a coverageData >= 5X
     There is a 10.58% of reference with a coverageData >= 6X
     There is a 10.58% of reference with a coverageData >= 7X
     There is a 10.58% of reference with a coverageData >= 8X
     There is a 10.58% of reference with a coverageData >= 9X
     There is a 10.58% of reference with a coverageData >= 10X
     There is a 10.58% of reference with a coverageData >= 11X
     There is a 10.58% of reference with a coverageData >= 12X
     There is a 10.58% of reference with a coverageData >= 13X
     There is a 10.58% of reference with a coverageData >= 14X
     There is a 10.58% of reference with a coverageData >= 15X
     There is a 10.58% of reference with a coverageData >= 16X
     There is a 10.58% of reference with a coverageData >= 17X
     There is a 10.58% of reference with a coverageData >= 18X
     There is a 10.58% of reference with a coverageData >= 19X
     There is a 10.58% of reference with a coverageData >= 20X
     There is a 10.58% of reference with a coverageData >= 21X
     There is a 10.58% of reference with a coverageData >= 22X
     There is a 10.58% of reference with a coverageData >= 23X
     There is a 10.58% of reference with a coverageData >= 24X
     There is a 10.58% of reference with a coverageData >= 25X
     There is a 10.58% of reference with a coverageData >= 26X
     There is a 10.58% of reference with a coverageData >= 27X
     There is a 10.58% of reference with a coverageData >= 28X
     There is a 10.58% of reference with a coverageData >= 29X
     There is a 10.58% of reference with a coverageData >= 30X
     There is a 10.58% of reference with a coverageData >= 31X
     There is a 10.1% of reference with a coverageData >= 32X
     There is a 9.62% of reference with a coverageData >= 33X
     There is a 9.13% of reference with a coverageData >= 34X
     There is a 7.21% of reference with a coverageData >= 35X
     There is a 5.29% of reference with a coverageData >= 36X
     There is a 3.37% of reference with a coverageData >= 37X
     There is a 1.44% of reference with a coverageData >= 38X
     There is a 0.96% 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	4424	6214	1.404611211573237	3.9981701358234454