
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192399_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 SRR3192399_1.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1694.98 s (22 us/read; 2.72 M reads/minute).

=== Summary ===

Total reads processed:              76,795,926
Reads with adapters:                27,726,219 (36.1%)
Reads written (passing filters):    76,795,926 (100.0%)

Total basepairs processed: 7,679,592,600 bp
Quality-trimmed:             306,342,809 bp (4.0%)
Total written (filtered):  7,304,196,164 bp (95.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 27726219 times.

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

Bases preceding removed adapters:
  A: 27.8%
  C: 34.5%
  G: 19.2%
  T: 18.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	17707434	19198981.5	0	17707434
2	5264485	4799745.4	0	5264485
3	1673429	1199936.3	0	1673429
4	526635	299984.1	0	526635
5	328087	74996.0	0	328087
6	234065	18749.0	0	234065
7	209903	4687.3	0	209903
8	185312	1171.8	0	185312
9	169127	293.0	0	167166 1961
10	151665	73.2	1	148352 3313
11	139504	18.3	1	137096 2408
12	139254	4.6	1	137219 2035
13	129286	1.1	1	127327 1959
14	115507	1.1	1	113611 1896
15	113426	1.1	1	111464 1962
16	84942	1.1	1	83503 1439
17	56751	1.1	1	55720 1031
18	41177	1.1	1	40447 730
19	38382	1.1	1	37742 640
20	37112	1.1	1	36424 688
21	31177	1.1	1	30655 522
22	28439	1.1	1	27906 533
23	25904	1.1	1	25452 452
24	25674	1.1	1	25179 495
25	27693	1.1	1	27204 489
26	25609	1.1	1	25115 494
27	21939	1.1	1	21413 526
28	18882	1.1	1	18459 423
29	15849	1.1	1	15507 342
30	14279	1.1	1	13931 348
31	10469	1.1	1	10220 249
32	10435	1.1	1	10194 241
33	10337	1.1	1	10063 274
34	19251	1.1	1	18764 487
35	10273	1.1	1	9986 287
36	7621	1.1	1	7416 205
37	7093	1.1	1	6881 212
38	7945	1.1	1	7685 260
39	6605	1.1	1	6360 245
40	5259	1.1	1	5065 194
41	5005	1.1	1	4847 158
42	3541	1.1	1	3444 97
43	3133	1.1	1	3021 112
44	2487	1.1	1	2388 99
45	2358	1.1	1	2267 91
46	2349	1.1	1	2228 121
47	2143	1.1	1	2051 92
48	1982	1.1	1	1854 128
49	1694	1.1	1	1611 83
50	1282	1.1	1	1200 82
51	1228	1.1	1	1125 103
52	947	1.1	1	838 109
53	761	1.1	1	706 55
54	515	1.1	1	462 53
55	450	1.1	1	399 51
56	655	1.1	1	558 97
57	1012	1.1	1	910 102
58	529	1.1	1	430 99
59	390	1.1	1	294 96
60	311	1.1	1	226 85
61	310	1.1	1	187 123
62	455	1.1	1	149 306
63	743	1.1	1	297 446
64	593	1.1	1	387 206
65	410	1.1	1	195 215
66	497	1.1	1	171 326
67	976	1.1	1	333 643
68	1636	1.1	1	516 1120
69	4312	1.1	1	805 3507
70	2834	1.1	1	1652 1182
71	1634	1.1	1	709 925
72	973	1.1	1	522 451
73	409	1.1	1	315 94
74	174	1.1	1	130 44
75	50	1.1	1	26 24
76	28	1.1	1	6 22
77	33	1.1	1	5 28
78	43	1.1	1	1 42
79	37	1.1	1	3 34
80	26	1.1	1	4 22
81	60	1.1	1	2 58
82	42	1.1	1	2 40
83	51	1.1	1	2 49
84	46	1.1	1	3 43
85	46	1.1	1	6 40
86	34	1.1	1	2 32
87	32	1.1	1	3 29
88	29	1.1	1	5 24
89	44	1.1	1	6 38
90	32	1.1	1	6 26
91	55	1.1	1	7 48
92	43	1.1	1	8 35
93	36	1.1	1	4 32
94	34	1.1	1	2 32
95	49	1.1	1	12 37
96	37	1.1	1	5 32
97	53	1.1	1	11 42
98	26	1.1	1	5 21
99	43	1.1	1	2 41
100	266	1.1	1	2 264


RUN STATISTICS FOR INPUT FILE: SRR3192399_1.fastq.gz
=============================================
76795926 sequences processed in total

