Mercurial > repos > iuc > qualimap_counts
diff test-data/genome_results_default.txt @ 0:e020be4f281b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
| author | iuc |
|---|---|
| date | Thu, 10 Oct 2019 17:40:46 -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 17:40:46 2019 -0400 @@ -0,0 +1,122 @@ +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 + +