1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
|
# Summary statistics, used for scaling the plots.
SS Number of files: 1
SS Number of amplicons: vir1 2
SS Reference length: vir1 800
SS End of summary
# Amplicon locations from BED file.
# LEFT/RIGHT are <start>-<end> format and comma-separated for alt-primers.
#
# AMPLICON REF NUMBER LEFT RIGHT
AMPLICON vir1 1 31-54 386-410
AMPLICON vir1 2 321-342 705-726
# Summary stats.
# Use 'grep ^FSS | cut -f 2-' to extract this part.
FSS mixed_clipped vir1 raw total sequences: 8
FSS mixed_clipped vir1 filtered sequences: 0
FSS mixed_clipped vir1 failed primer match: 2
FSS mixed_clipped vir1 matching sequences: 6
FSS mixed_clipped vir1 consensus depth count < 1 and >= 1: 132 517
# Absolute matching read counts per amplicon.
# Use 'grep ^FREADS | cut -f 2-' to extract this part.
FREADS mixed_clipped 5 1
FVDEPTH mixed_clipped 2 0
# Read percentage of distribution between amplicons.
# Use 'grep ^FRPERC | cut -f 2-' to extract this part.
FRPERC mixed_clipped 83.333 16.667
# Read depth per amplicon.
# Use 'grep ^FDEPTH | cut -f 2-' to extract this part.
FDEPTH mixed_clipped 2.8 0.5
# Percentage coverage per amplicon
# Use 'grep ^FPCOV | cut -f 2-' to extract this part.
FPCOV-1 mixed_clipped 100.00 51.80
# Depth per reference base for ALL data.
# Use 'grep ^FDP_ALL | cut -f 2-' to extract this part.
FDP_ALL mixed_clipped vir1 0,54 2,77 3,254 0,25 1,294 0,96
# Depth per reference base for full-length valid amplicon data.
# Use 'grep ^FDP_VALID | cut -f 2-' to extract this part.
FDP_VALID mixed_clipped vir1 0,54 2,331 0,415
# Distribution of aligned template coordinates.
# Use 'grep ^FTCOORD | cut -f 2-' to extract this part.
FTCOORD mixed_clipped 1 55,385,2,0
FTCOORD mixed_clipped 2
# Classification of amplicon status. Columns are
# number with both primers from this amplicon, number with
# primers from different amplicon, and number with a position
# not matching any valid amplicon primer site
# Use 'grep ^FAMP | cut -f 2-' to extract this part.
FAMP mixed_clipped 0 2 0 2
FAMP mixed_clipped 1 2 0 1
FAMP mixed_clipped 2 0 0 1
# Summary stats.
# Use 'grep ^CSS | cut -f 2-' to extract this part.
CSS COMBINED vir1 raw total sequences: 8
CSS COMBINED vir1 filtered sequences: 0
CSS COMBINED vir1 failed primer match: 2
CSS COMBINED vir1 matching sequences: 6
CSS COMBINED vir1 consensus depth count < 1 and >= 1: 649 0
# Absolute matching read counts per amplicon.
# Use 'grep ^CREADS | cut -f 2-' to extract this part.
CREADS COMBINED 5 1
CVDEPTH COMBINED 2 0
CREADS MEAN 5.0 1.0
CREADS STDDEV 0.0 0.0
# Read percentage of distribution between amplicons.
# Use 'grep ^CRPERC | cut -f 2-' to extract this part.
CRPERC COMBINED 83.333 16.667
CRPERC MEAN 83.333 16.667
CRPERC STDDEV 0.000 0.000
# Read depth per amplicon.
# Use 'grep ^CDEPTH | cut -f 2-' to extract this part.
CDEPTH COMBINED 2.8 0.5
CDEPTH MEAN 2.8 0.5
CDEPTH STDDEV 0.0 0.0
CPCOV-1 MEAN 100.0 51.8
CPCOV-1 STDDEV 0.0 0.0
# Depth per reference base for ALL data.
# Use 'grep ^CDP_ALL | cut -f 2-' to extract this part.
CDP_ALL COMBINED vir1 0,54 2,77 3,254 0,25 1,294 0,96
# Depth per reference base for full-length valid amplicon data.
# Use 'grep ^CDP_VALID | cut -f 2-' to extract this part.
CDP_VALID COMBINED vir1 0,54 2,331 0,415
# Distribution of aligned template coordinates.
# Use 'grep ^CTCOORD | cut -f 2-' to extract this part.
CTCOORD COMBINED 1 55,385,2,0
CTCOORD COMBINED 2
# Classification of amplicon status. Columns are
# number with both primers from this amplicon, number with
# primers from different amplicon, and number with a position
# not matching any valid amplicon primer site
# Use 'grep ^CAMP | cut -f 2-' to extract this part.
CAMP COMBINED 0 2 0 2
CAMP COMBINED 1 2 0 1
CAMP COMBINED 2 0 0 1
|
