Mercurial > repos > iuc > multiqc

comparison test-data/genome_results.txt @ 16:bf675f34b056 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
author iuc
date Sat, 16 May 2020 09:40:45 -0400
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15:3d93dd18d9f8 16:bf675f34b056
1 BamQC report
2 -----------------------------------
3
4 >>>>>>> Input
5
6 bam file = x_bam
7 outfile = results/genome_results.txt
8
9
10 >>>>>>> Reference
11
12 number of bases = 1,817,261 bp
13 number of contigs = 1
14
15
16 >>>>>>> Globals
17
18 number of windows = 400
19
20 number of reads = 1,248,774
21 number of mapped reads = 1,242,183 (99.47%)
22 number of supplementary alignments = 3,386 (0.27%)
23 number of secondary alignments = 0
24
25 number of mapped paired reads (first in pair) = 623,192
26 number of mapped paired reads (second in pair) = 618,991
27 number of mapped paired reads (both in pair) = 1,237,764
28 number of mapped paired reads (singletons) = 4,419
29 number of overlapping read pairs = 463,596
30
31 number of mapped bases = 366,875,582 bp
32 number of sequenced bases = 366,823,893 bp
33 number of aligned bases = 0 bp
34 number of duplicated reads (estimated) = 673,527
35 duplication rate = 47.01%
36
37
38 >>>>>>> Insert size
39
40 mean insert size = 1,097.678
41 std insert size = 27,365.2401
42 median insert size = 524
43
44
45 >>>>>>> Mapping quality
46
47 mean mapping quality = 58.4552
48
49
50 >>>>>>> ACTG content
51
52 number of A's = 109,576,306 bp (29.87%)
53 number of C's = 73,524,910 bp (20.04%)
54 number of T's = 111,308,231 bp (30.34%)
55 number of G's = 72,414,446 bp (19.74%)
56 number of N's = 0 bp (0%)
57
58 GC percentage = 39.78%
59
60
61 >>>>>>> Mismatches and indels
62
63 general error rate = 0.0098
64 number of mismatches = 3,560,959
65 number of insertions = 7,229
66 mapped reads with insertion percentage = 0.56%
67 number of deletions = 14,669
68 mapped reads with deletion percentage = 1.15%
69 homopolymer indels = 46.92%
70
71
72 >>>>>>> Coverage
73
74 mean coverageData = 201.8838X
75 std coverageData = 112.2733X
76 paired-end adapted mean coverage = 177.4988X
77
78 There is a 99.81% of reference with a coverageData >= 1X
79 There is a 99.77% of reference with a coverageData >= 2X
80 There is a 99.74% of reference with a coverageData >= 3X
81 There is a 99.7% of reference with a coverageData >= 4X
82 There is a 99.66% of reference with a coverageData >= 5X
83 There is a 99.6% of reference with a coverageData >= 6X
84 There is a 99.53% of reference with a coverageData >= 7X
85 There is a 99.41% of reference with a coverageData >= 8X
86 There is a 99.3% of reference with a coverageData >= 9X
87 There is a 99.21% of reference with a coverageData >= 10X
88 There is a 99.11% of reference with a coverageData >= 11X
89 There is a 98.99% of reference with a coverageData >= 12X
90 There is a 98.87% of reference with a coverageData >= 13X
91 There is a 98.76% of reference with a coverageData >= 14X
92 There is a 98.63% of reference with a coverageData >= 15X
93 There is a 98.5% of reference with a coverageData >= 16X
94 There is a 98.35% of reference with a coverageData >= 17X
95 There is a 98.16% of reference with a coverageData >= 18X
96 There is a 97.97% of reference with a coverageData >= 19X
97 There is a 97.79% of reference with a coverageData >= 20X
98 There is a 97.59% of reference with a coverageData >= 21X
99 There is a 97.37% of reference with a coverageData >= 22X
100 There is a 97.16% of reference with a coverageData >= 23X
101 There is a 96.95% of reference with a coverageData >= 24X
102 There is a 96.71% of reference with a coverageData >= 25X
103 There is a 96.48% of reference with a coverageData >= 26X
104 There is a 96.24% of reference with a coverageData >= 27X
105 There is a 95.99% of reference with a coverageData >= 28X
106 There is a 95.73% of reference with a coverageData >= 29X
107 There is a 95.49% of reference with a coverageData >= 30X
108 There is a 95.23% of reference with a coverageData >= 31X
109 There is a 94.99% of reference with a coverageData >= 32X
110 There is a 94.75% of reference with a coverageData >= 33X
111 There is a 94.51% of reference with a coverageData >= 34X
112 There is a 94.27% of reference with a coverageData >= 35X
113 There is a 94.01% of reference with a coverageData >= 36X
114 There is a 93.8% of reference with a coverageData >= 37X
115 There is a 93.55% of reference with a coverageData >= 38X
116 There is a 93.31% of reference with a coverageData >= 39X
117 There is a 93.04% of reference with a coverageData >= 40X
118 There is a 92.77% of reference with a coverageData >= 41X
119 There is a 92.52% of reference with a coverageData >= 42X
120 There is a 92.27% of reference with a coverageData >= 43X
121 There is a 91.99% of reference with a coverageData >= 44X
122 There is a 91.72% of reference with a coverageData >= 45X
123 There is a 91.44% of reference with a coverageData >= 46X
124 There is a 91.17% of reference with a coverageData >= 47X
125 There is a 90.9% of reference with a coverageData >= 48X
126 There is a 90.64% of reference with a coverageData >= 49X
127 There is a 90.4% of reference with a coverageData >= 50X
128 There is a 90.15% of reference with a coverageData >= 51X
129
130
131 >>>>>>> Coverage per contig
132
133 NZ_CP031250.1 1817261 366875582 201.88381415768015 112.27329056357358
134
135