Mercurial > repos > iuc > qualimap_counts

comparison test-data/genome_results_inside_features.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/tmpB4Sf0A/files/e/d/7/dataset_ed7510d4-c8f3-41fc-8cc1-3b854d9bdf14.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 = 6,451 bp
25 number of sequenced bases = 5,101 bp
26 number of aligned bases = 0 bp
27 number of duplicated reads (estimated) = 14
28 duplication rate = 16.18%
29
30
31 >>>>>>> Globals inside
32
33 regions size = 300 (46.15%)
34 number of mapped reads = 82 (82%)
35
36
37 >>>>>>> Insert size
38
39 mean insert size = 0
40 std insert size = 0
41 median insert size = 0
42
43
44 >>>>>>> Mapping quality
45
46 mean mapping quality = 251.3687
47
48
49 >>>>>>> ACTG content
50
51 number of A's = 1,243 bp (24.37%)
52 number of C's = 1,257 bp (24.64%)
53 number of T's = 985 bp (19.31%)
54 number of G's = 1,616 bp (31.68%)
55 number of N's = 0 bp (0%)
56
57 GC percentage = 56.32%
58
59
60 >>>>>>> Mismatches and indels
61
62 general error rate = 0.0211
63 number of mismatches = 136
64
65
66 >>>>>>> Coverage
67
68 mean coverageData = 21.5033X
69 std coverageData = 15.658X
70
71 There is a 66% of reference with a coverageData >= 1X
72 There is a 65.33% of reference with a coverageData >= 2X
73 There is a 65% of reference with a coverageData >= 3X
74 There is a 64.33% of reference with a coverageData >= 4X
75 There is a 63.33% of reference with a coverageData >= 5X
76 There is a 59.67% of reference with a coverageData >= 6X
77 There is a 57.67% of reference with a coverageData >= 7X
78 There is a 57.67% of reference with a coverageData >= 8X
79 There is a 56% of reference with a coverageData >= 9X
80 There is a 55% of reference with a coverageData >= 10X
81 There is a 54.33% of reference with a coverageData >= 11X
82 There is a 54% of reference with a coverageData >= 12X
83 There is a 53.33% of reference with a coverageData >= 13X
84 There is a 53% of reference with a coverageData >= 14X
85 There is a 52.33% of reference with a coverageData >= 15X
86 There is a 52.33% of reference with a coverageData >= 16X
87 There is a 51.67% of reference with a coverageData >= 17X
88 There is a 51% of reference with a coverageData >= 18X
89 There is a 50% of reference with a coverageData >= 19X
90 There is a 50% of reference with a coverageData >= 20X
91 There is a 50% of reference with a coverageData >= 21X
92 There is a 49.67% of reference with a coverageData >= 22X
93 There is a 49.33% of reference with a coverageData >= 23X
94 There is a 48.33% of reference with a coverageData >= 24X
95 There is a 48% of reference with a coverageData >= 25X
96 There is a 45.33% of reference with a coverageData >= 26X
97 There is a 43% of reference with a coverageData >= 27X
98 There is a 42% of reference with a coverageData >= 28X
99 There is a 39.33% of reference with a coverageData >= 29X
100 There is a 35.67% of reference with a coverageData >= 30X
101 There is a 32.33% of reference with a coverageData >= 31X
102 There is a 25.67% of reference with a coverageData >= 32X
103 There is a 16.67% of reference with a coverageData >= 33X
104 There is a 13% of reference with a coverageData >= 34X
105 There is a 11.33% of reference with a coverageData >= 35X
106 There is a 10% of reference with a coverageData >= 36X
107 There is a 5.67% of reference with a coverageData >= 37X
108 There is a 3% of reference with a coverageData >= 38X
109 There is a 0% of reference with a coverageData >= 39X
110 There is a 0% of reference with a coverageData >= 40X
111 There is a 0% of reference with a coverageData >= 41X
112 There is a 0% of reference with a coverageData >= 42X
113 There is a 0% of reference with a coverageData >= 43X
114 There is a 0% of reference with a coverageData >= 44X
115 There is a 0% of reference with a coverageData >= 45X
116 There is a 0% of reference with a coverageData >= 46X
117 There is a 0% of reference with a coverageData >= 47X
118 There is a 0% of reference with a coverageData >= 48X
119 There is a 0% of reference with a coverageData >= 49X
120 There is a 0% of reference with a coverageData >= 50X
121 There is a 0% of reference with a coverageData >= 51X
122
123
124 >>>>>>> Coverage per contig
125
126 test_chromosome 300 6451 21.503333333333334 15.658011438947867
127
128