Mercurial > repos > iuc > qualimap_counts

comparison test-data/genome_results_outside_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/tmprT4oZK/files/6/4/1/dataset_6416c0ca-3ecd-4273-ae01-22f2ac60965d.dat
7 outfile = results/outside_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 = 6,214 bp
25 number of sequenced bases = 2,364 bp
26 number of aligned bases = 0 bp
27 number of duplicated reads (estimated) = 4
28 duplication rate = 14.29%
29
30
31 >>>>>>> Globals outside
32
33 regions size = 350 (53.85%)
34 number of mapped reads = 18 (18%)
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 = 255
47
48
49 >>>>>>> ACTG content
50
51 number of A's = 667 bp (28.21%)
52 number of C's = 645 bp (27.28%)
53 number of T's = 512 bp (21.66%)
54 number of G's = 540 bp (22.84%)
55 number of N's = 0 bp (0%)
56
57 GC percentage = 50.13%
58
59
60 >>>>>>> Mismatches and indels
61
62 general error rate = 0.0021
63 number of mismatches = 13
64
65
66 >>>>>>> Coverage
67
68 mean coverageData = 17.7543X
69 std coverageData = 16.4764X
70
71 There is a 10.58% of reference with a coverageData >= 1X
72 There is a 10.58% of reference with a coverageData >= 2X
73 There is a 10.58% of reference with a coverageData >= 3X
74 There is a 10.58% of reference with a coverageData >= 4X
75 There is a 10.58% of reference with a coverageData >= 5X
76 There is a 10.58% of reference with a coverageData >= 6X
77 There is a 10.58% of reference with a coverageData >= 7X
78 There is a 10.58% of reference with a coverageData >= 8X
79 There is a 10.58% of reference with a coverageData >= 9X
80 There is a 10.58% of reference with a coverageData >= 10X
81 There is a 10.58% of reference with a coverageData >= 11X
82 There is a 10.58% of reference with a coverageData >= 12X
83 There is a 10.58% of reference with a coverageData >= 13X
84 There is a 10.58% of reference with a coverageData >= 14X
85 There is a 10.58% of reference with a coverageData >= 15X
86 There is a 10.58% of reference with a coverageData >= 16X
87 There is a 10.58% of reference with a coverageData >= 17X
88 There is a 10.58% of reference with a coverageData >= 18X
89 There is a 10.58% of reference with a coverageData >= 19X
90 There is a 10.58% of reference with a coverageData >= 20X
91 There is a 10.58% of reference with a coverageData >= 21X
92 There is a 10.58% of reference with a coverageData >= 22X
93 There is a 10.58% of reference with a coverageData >= 23X
94 There is a 10.58% of reference with a coverageData >= 24X
95 There is a 10.58% of reference with a coverageData >= 25X
96 There is a 10.58% of reference with a coverageData >= 26X
97 There is a 10.58% of reference with a coverageData >= 27X
98 There is a 10.58% of reference with a coverageData >= 28X
99 There is a 10.58% of reference with a coverageData >= 29X
100 There is a 10.58% of reference with a coverageData >= 30X
101 There is a 10.58% of reference with a coverageData >= 31X
102 There is a 10.1% of reference with a coverageData >= 32X
103 There is a 9.62% of reference with a coverageData >= 33X
104 There is a 9.13% of reference with a coverageData >= 34X
105 There is a 7.21% of reference with a coverageData >= 35X
106 There is a 5.29% of reference with a coverageData >= 36X
107 There is a 3.37% of reference with a coverageData >= 37X
108 There is a 1.44% of reference with a coverageData >= 38X
109 There is a 0.96% 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 4424 6214 1.404611211573237 3.9981701358234454
127
128