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
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
|
# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
CHK cb2d2d82 bcd83869 d22eda06
# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
SN raw total sequences: 26 # excluding supplementary and secondary reads
SN filtered sequences: 0
SN sequences: 26
SN is sorted: 1 # sorted by coordinate
SN 1st fragments: 14
SN last fragments: 12
SN reads mapped: 26
SN reads mapped and paired: 26 # paired-end technology bit set + both mates mapped
SN reads unmapped: 0
SN reads properly paired: 24 # proper-pair bit set
SN reads paired: 26 # paired-end technology bit set
SN reads duplicated: 0 # PCR or optical duplicate bit set
SN reads MQ0: 1 # mapped and MQ=0
SN reads QC failed: 0
SN non-primary alignments: 0
SN supplementary alignments: 0
SN total length: 260 # ignores clipping
SN total first fragment length: 140 # ignores clipping
SN total last fragment length: 120 # ignores clipping
SN bases mapped: 260 # ignores clipping
SN bases mapped (cigar): 206 # more accurate
SN bases trimmed: 0
SN bases duplicated: 0
SN mismatches: 0 # from NM fields
SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar)
SN average length: 10
SN average first fragment length: 10
SN average last fragment length: 10
SN maximum length: 10
SN maximum first fragment length: 10
SN maximum last fragment length: 10
SN average quality: 13.1
SN insert size average: 34.0
SN insert size standard deviation: 0.0
SN inward oriented pairs: 12
SN outward oriented pairs: 0
SN pairs with other orientation: 0
SN pairs on different chromosomes: 1
SN percentage of properly paired reads (%): 92.3
SN bases inside the target: 42
SN percentage of target genome with coverage > 0 (%): 100.00
# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part.
# Columns correspond to qualities and rows to cycles. First column is the cycle number.
FFQ 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
FFQ 2 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
FFQ 3 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
FFQ 4 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
FFQ 5 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
FFQ 6 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
FFQ 7 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
FFQ 8 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
FFQ 9 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
FFQ 10 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0
# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part.
# Columns correspond to qualities and rows to cycles. First column is the cycle number.
LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0
# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.
GCF 19.85 0
GCF 44.72 1
GCF 54.77 4
GCF 64.82 2
GCF 74.87 4
GCF 84.92 3
# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.
GCL 19.85 0
GCL 44.72 2
GCL 59.80 3
GCL 74.87 4
# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
GCC 1 19.23 42.31 15.38 23.08 0.00 0.00
GCC 2 19.23 19.23 46.15 15.38 0.00 0.00
GCC 3 23.08 38.46 19.23 19.23 0.00 0.00
GCC 4 23.08 23.08 38.46 15.38 0.00 0.00
GCC 5 11.54 38.46 26.92 23.08 0.00 0.00
GCC 6 23.08 23.08 34.62 19.23 0.00 0.00
GCC 7 15.38 34.62 26.92 23.08 0.00 0.00
GCC 8 26.92 23.08 38.46 11.54 0.00 0.00
GCC 9 23.08 26.92 26.92 23.08 0.00 0.00
GCC 10 23.08 23.08 38.46 15.38 0.00 0.00
# ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]
GCT 1 26.92 26.92 30.77 15.38
GCT 2 7.69 38.46 26.92 26.92
GCT 3 26.92 26.92 30.77 15.38
GCT 4 11.54 34.62 26.92 26.92
GCT 5 23.08 26.92 38.46 11.54
GCT 6 11.54 34.62 23.08 30.77
GCT 7 19.23 23.08 38.46 19.23
GCT 8 11.54 38.46 23.08 26.92
GCT 9 23.08 19.23 34.62 23.08
GCT 10 11.54 34.62 26.92 26.92
# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
FBC 1 21.43 42.86 21.43 14.29 0.00 0.00
FBC 2 7.14 28.57 42.86 21.43 0.00 0.00
FBC 3 28.57 35.71 21.43 14.29 0.00 0.00
FBC 4 14.29 28.57 35.71 21.43 0.00 0.00
FBC 5 14.29 35.71 35.71 14.29 0.00 0.00
FBC 6 14.29 28.57 28.57 28.57 0.00 0.00
FBC 7 14.29 28.57 35.71 21.43 0.00 0.00
FBC 8 21.43 28.57 28.57 21.43 0.00 0.00
FBC 9 21.43 21.43 35.71 21.43 0.00 0.00
FBC 10 14.29 28.57 35.71 21.43 0.00 0.00
# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
FTC 24 43 45 28 0
# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
LBC 1 16.67 41.67 8.33 33.33 0.00 0.00
LBC 2 33.33 8.33 50.00 8.33 0.00 0.00
LBC 3 16.67 41.67 16.67 25.00 0.00 0.00
LBC 4 33.33 16.67 41.67 8.33 0.00 0.00
LBC 5 8.33 41.67 16.67 33.33 0.00 0.00
LBC 6 33.33 16.67 41.67 8.33 0.00 0.00
LBC 7 16.67 41.67 16.67 25.00 0.00 0.00
LBC 8 33.33 16.67 50.00 0.00 0.00 0.00
LBC 9 25.00 33.33 16.67 25.00 0.00 0.00
LBC 10 33.33 16.67 41.67 8.33 0.00 0.00
# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
LTC 30 33 36 21 0
# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
IS 0 0 0 0 0
IS 1 0 0 0 0
IS 2 0 0 0 0
IS 3 0 0 0 0
IS 4 0 0 0 0
IS 5 0 0 0 0
IS 6 0 0 0 0
IS 7 0 0 0 0
IS 8 0 0 0 0
IS 9 0 0 0 0
IS 10 0 0 0 0
IS 11 0 0 0 0
IS 12 0 0 0 0
IS 13 0 0 0 0
IS 14 0 0 0 0
IS 15 0 0 0 0
IS 16 0 0 0 0
IS 17 0 0 0 0
IS 18 0 0 0 0
IS 19 0 0 0 0
IS 20 0 0 0 0
IS 21 0 0 0 0
IS 22 0 0 0 0
IS 23 0 0 0 0
IS 24 0 0 0 0
IS 25 0 0 0 0
IS 26 0 0 0 0
IS 27 0 0 0 0
IS 28 0 0 0 0
IS 29 0 0 0 0
IS 30 0 0 0 0
IS 31 0 0 0 0
IS 32 0 0 0 0
IS 33 0 0 0 0
IS 34 12 12 0 0
# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
RL 10 26
# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
FRL 10 14
# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count
LRL 10 12
# Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count
MAPQ 0 1
MAPQ 1 1
MAPQ 2 1
MAPQ 3 1
MAPQ 4 1
MAPQ 5 1
MAPQ 6 1
MAPQ 7 1
MAPQ 8 1
MAPQ 9 1
MAPQ 10 1
MAPQ 11 1
MAPQ 12 1
MAPQ 13 1
MAPQ 14 1
MAPQ 15 1
MAPQ 16 1
MAPQ 17 1
MAPQ 18 1
MAPQ 19 1
MAPQ 20 1
MAPQ 21 1
MAPQ 22 1
MAPQ 23 1
MAPQ 50 2
# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)
# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.
COV [1-1] 1 1
COV [2-2] 2 1
COV [3-3] 3 2
COV [4-4] 4 2
COV [5-5] 5 23
COV [6-6] 6 13
# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile
GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000
|
