diff test-data/genome_results_default.txt @ 0:613e6446ea5d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
author iuc
date Thu, 10 Oct 2019 17:41:10 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_default.txt	Thu Oct 10 17:41:10 2019 -0400
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+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
+
+