
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192398_1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.1
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Running FastQC on the data once trimming has completed
Output file will be GZIP compressed


This is cutadapt 1.9.1 with Python 2.7.6
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192398_1.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1558.02 s (23 us/read; 2.65 M reads/minute).

=== Summary ===

Total reads processed:              68,765,938
Reads with adapters:                24,776,219 (36.0%)
Reads written (passing filters):    68,765,938 (100.0%)

Total basepairs processed: 6,876,593,800 bp
Quality-trimmed:             278,227,662 bp (4.0%)
Total written (filtered):  6,538,840,170 bp (95.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24776219 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 28.4%
  C: 34.1%
  G: 18.8%
  T: 18.7%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	16021271	17191484.5	0	16021271
2	4699932	4297871.1	0	4699932
3	1508602	1074467.8	0	1508602
4	453513	268616.9	0	453513
5	273388	67154.2	0	273388
6	191192	16788.6	0	191192
7	169275	4197.1	0	169275
8	150430	1049.3	0	150430
9	139426	262.3	0	137722 1704
10	122228	65.6	1	119552 2676
11	112758	16.4	1	110925 1833
12	110789	4.1	1	109262 1527
13	102395	1.0	1	100897 1498
14	84764	1.0	1	83584 1180
15	80197	1.0	1	78962 1235
16	75853	1.0	1	74641 1212
17	56820	1.0	1	55824 996
18	43570	1.0	1	42851 719
19	33410	1.0	1	32909 501
20	27061	1.0	1	26606 455
21	23822	1.0	1	23424 398
22	25845	1.0	1	25377 468
23	27296	1.0	1	26836 460
24	24317	1.0	1	23890 427
25	19752	1.0	1	19462 290
26	18553	1.0	1	18238 315
27	17968	1.0	1	17560 408
28	20792	1.0	1	20388 404
29	14527	1.0	1	14226 301
30	11801	1.0	1	11520 281
31	9414	1.0	1	9202 212
32	8692	1.0	1	8464 228
33	7743	1.0	1	7554 189
34	15277	1.0	1	14882 395
35	7217	1.0	1	7004 213
36	6097	1.0	1	5907 190
37	5269	1.0	1	5096 173
38	6084	1.0	1	5893 191
39	5045	1.0	1	4859 186
40	4900	1.0	1	4728 172
41	4024	1.0	1	3890 134
42	2218	1.0	1	2143 75
43	1554	1.0	1	1508 46
44	1651	1.0	1	1585 66
45	1544	1.0	1	1478 66
46	1849	1.0	1	1747 102
47	1504	1.0	1	1438 66
48	1213	1.0	1	1140 73
49	1085	1.0	1	1030 55
50	721	1.0	1	664 57
51	628	1.0	1	569 59
52	557	1.0	1	466 91
53	452	1.0	1	404 48
54	351	1.0	1	298 53
55	244	1.0	1	195 49
56	269	1.0	1	208 61
57	249	1.0	1	181 68
58	342	1.0	1	235 107
59	374	1.0	1	285 89
60	271	1.0	1	156 115
61	279	1.0	1	166 113
62	431	1.0	1	134 297
63	709	1.0	1	259 450
64	542	1.0	1	331 211
65	397	1.0	1	165 232
66	556	1.0	1	179 377
67	1036	1.0	1	264 772
68	1885	1.0	1	462 1423
69	4722	1.0	1	684 4038
70	2904	1.0	1	1397 1507
71	1746	1.0	1	613 1133
72	1062	1.0	1	489 573
73	324	1.0	1	239 85
74	159	1.0	1	124 35
75	60	1.0	1	32 28
76	18	1.0	1	7 11
77	22	1.0	1	5 17
78	43	1.0	1	5 38
79	37	1.0	1	1 36
80	29	1.0	1	5 24
81	38	1.0	1	1 37
82	32	1.0	1	0 32
83	43	1.0	1	2 41
84	33	1.0	1	3 30
85	35	1.0	1	4 31
86	33	1.0	1	0 33
87	31	1.0	1	2 29
88	34	1.0	1	7 27
89	33	1.0	1	2 31
90	32	1.0	1	3 29
91	43	1.0	1	5 38
92	28	1.0	1	4 24
93	29	1.0	1	3 26
94	29	1.0	1	3 26
95	54	1.0	1	14 40
96	32	1.0	1	7 25
97	38	1.0	1	5 33
98	25	1.0	1	2 23
99	33	1.0	1	3 30
100	218	1.0	1	1 217


RUN STATISTICS FOR INPUT FILE: SRR3192398_1.fastq.gz
=============================================
68765938 sequences processed in total

