Mercurial > repos > iuc > qualimap_counts

comparison test-data/genome_results_default.txt @ 0:e020be4f281b draft

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"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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-1:000000000000 0:e020be4f281b
1 BamQC report
2 -----------------------------------
3
4 >>>>>>> Input
5
6 bam file = /tmp/tmprT4oZK/files/b/1/f/dataset_b1fbaad4-1b5a-4769-8a15-b4cec4de5731.dat
7 outfile = results/genome_results.txt
8
9
10 >>>>>>> Reference
11
12 number of bases = 650 bp
13 number of contigs = 1
14
15
16 >>>>>>> Globals
17
18 number of windows = 325
19
20 number of reads = 100
21 number of mapped reads = 100 (100%)
22 number of secondary alignments = 1
23
24 number of mapped bases = 12,665 bp
25 number of sequenced bases = 7,465 bp
26 number of aligned bases = 0 bp
27 number of duplicated reads (estimated) = 18
28 duplication rate = 15.85%
29
30
31 >>>>>>> Insert size
32
33 mean insert size = 0
34 std insert size = 0
35 median insert size = 0
36
37
38 >>>>>>> Mapping quality
39
40 mean mapping quality = 115.8402
41
42
43 >>>>>>> ACTG content
44
45 number of A's = 1,910 bp (25.59%)
46 number of C's = 1,902 bp (25.48%)
47 number of T's = 1,497 bp (20.05%)
48 number of G's = 2,156 bp (28.88%)
49 number of N's = 0 bp (0%)
50
51 GC percentage = 54.36%
52
53
54 >>>>>>> Mismatches and indels
55
56 general error rate = 0.0118
57 number of mismatches = 149
58
59
60 >>>>>>> Coverage
61
62 mean coverageData = 19.4846X
63 std coverageData = 16.5813X
64
65 There is a 45.85% of reference with a coverageData >= 1X
66 There is a 45.38% of reference with a coverageData >= 2X
67 There is a 44.92% of reference with a coverageData >= 3X
68 There is a 44.62% of reference with a coverageData >= 4X
69 There is a 43.85% of reference with a coverageData >= 5X
70 There is a 41.85% of reference with a coverageData >= 6X
71 There is a 40.46% of reference with a coverageData >= 7X
72 There is a 39.85% of reference with a coverageData >= 8X
73 There is a 38.77% of reference with a coverageData >= 9X
74 There is a 38% of reference with a coverageData >= 10X
75 There is a 37.23% of reference with a coverageData >= 11X
76 There is a 36.92% of reference with a coverageData >= 12X
77 There is a 36.46% of reference with a coverageData >= 13X
78 There is a 36.15% of reference with a coverageData >= 14X
79 There is a 35.54% of reference with a coverageData >= 15X
80 There is a 35.23% of reference with a coverageData >= 16X
81 There is a 34.77% of reference with a coverageData >= 17X
82 There is a 34% of reference with a coverageData >= 18X
83 There is a 33.38% of reference with a coverageData >= 19X
84 There is a 33.38% of reference with a coverageData >= 20X
85 There is a 33.23% of reference with a coverageData >= 21X
86 There is a 31.85% of reference with a coverageData >= 22X
87 There is a 31.54% of reference with a coverageData >= 23X
88 There is a 30.92% of reference with a coverageData >= 24X
89 There is a 30.62% of reference with a coverageData >= 25X
90 There is a 28.62% of reference with a coverageData >= 26X
91 There is a 27.54% of reference with a coverageData >= 27X
92 There is a 26.92% of reference with a coverageData >= 28X
93 There is a 25.23% of reference with a coverageData >= 29X
94 There is a 23.38% of reference with a coverageData >= 30X
95 There is a 20.77% of reference with a coverageData >= 31X
96 There is a 16.77% of reference with a coverageData >= 32X
97 There is a 12.15% of reference with a coverageData >= 33X
98 There is a 10.15% of reference with a coverageData >= 34X
99 There is a 8.62% of reference with a coverageData >= 35X
100 There is a 7.38% of reference with a coverageData >= 36X
101 There is a 4% of reference with a coverageData >= 37X
102 There is a 1.85% of reference with a coverageData >= 38X
103 There is a 0.31% of reference with a coverageData >= 39X
104 There is a 0% of reference with a coverageData >= 40X
105 There is a 0% of reference with a coverageData >= 41X
106 There is a 0% of reference with a coverageData >= 42X
107 There is a 0% of reference with a coverageData >= 43X
108 There is a 0% of reference with a coverageData >= 44X
109 There is a 0% of reference with a coverageData >= 45X
110 There is a 0% of reference with a coverageData >= 46X
111 There is a 0% of reference with a coverageData >= 47X
112 There is a 0% of reference with a coverageData >= 48X
113 There is a 0% of reference with a coverageData >= 49X
114 There is a 0% of reference with a coverageData >= 50X
115 There is a 0% of reference with a coverageData >= 51X
116
117
118 >>>>>>> Coverage per contig
119
120 test_chromosome 650 12665 19.484615384615385 16.581284452141826
121
122