
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192399_2.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_2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1693.72 s (22 us/read; 2.72 M reads/minute).

=== Summary ===

Total reads processed:              76,795,926
Reads with adapters:                28,921,721 (37.7%)
Reads written (passing filters):    76,795,926 (100.0%)

Total basepairs processed: 7,679,592,600 bp
Quality-trimmed:             314,228,271 bp (4.1%)
Total written (filtered):  7,294,474,633 bp (95.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 28921721 times.

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

Bases preceding removed adapters:
  A: 32.3%
  C: 29.8%
  G: 21.4%
  T: 16.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	18364094	19198981.5	0	18364094
2	5573442	4799745.4	0	5573442
3	1839567	1199936.3	0	1839567
4	586513	299984.1	0	586513
5	311512	74996.0	0	311512
6	231259	18749.0	0	231259
7	211269	4687.3	0	211269
8	185719	1171.8	0	185719
9	174550	293.0	0	172950 1600
10	154985	73.2	1	149922 5063
11	142105	18.3	1	138230 3875
12	142397	4.6	1	139031 3366
13	135460	1.1	1	132182 3278
14	123946	1.1	1	120845 3101
15	108713	1.1	1	105979 2734
16	85595	1.1	1	83358 2237
17	59538	1.1	1	57791 1747
18	37746	1.1	1	36576 1170
19	40443	1.1	1	39278 1165
20	35097	1.1	1	34063 1034
21	29645	1.1	1	28792 853
22	27714	1.1	1	26896 818
23	26823	1.1	1	26006 817
24	30372	1.1	1	29461 911
25	27023	1.1	1	26202 821
26	25668	1.1	1	24811 857
27	22605	1.1	1	21883 722
28	20460	1.1	1	19824 636
29	16473	1.1	1	15974 499
30	21981	1.1	1	21299 682
31	7451	1.1	1	7216 235
32	9399	1.1	1	9122 277
33	8200	1.1	1	7941 259
34	16270	1.1	1	15857 413
35	9141	1.1	1	8839 302
36	7140	1.1	1	6880 260
37	6626	1.1	1	6412 214
38	7222	1.1	1	6992 230
39	6259	1.1	1	6023 236
40	5123	1.1	1	4946 177
41	4731	1.1	1	4513 218
42	4934	1.1	1	4739 195
43	3012	1.1	1	2857 155
44	2781	1.1	1	2625 156
45	2728	1.1	1	2582 146
46	1860	1.1	1	1756 104
47	2073	1.1	1	1968 105
48	1820	1.1	1	1731 89
49	1549	1.1	1	1468 81
50	1481	1.1	1	1389 92
51	1432	1.1	1	1312 120
52	678	1.1	1	596 82
53	525	1.1	1	473 52
54	555	1.1	1	480 75
55	506	1.1	1	439 67
56	617	1.1	1	542 75
57	1017	1.1	1	942 75
58	618	1.1	1	525 93
59	422	1.1	1	364 58
60	462	1.1	1	375 87
61	388	1.1	1	304 84
62	529	1.1	1	406 123
63	1300	1.1	1	1004 296
64	2261	1.1	1	1647 614
65	3841	1.1	1	2884 957
66	1656	1.1	1	1234 422
67	212	1.1	1	159 53
68	116	1.1	1	56 60
69	103	1.1	1	20 83
70	68	1.1	1	16 52
71	72	1.1	1	8 64
72	40	1.1	1	6 34
73	65	1.1	1	7 58
74	55	1.1	1	4 51
75	54	1.1	1	5 49
76	73	1.1	1	6 67
77	42	1.1	1	2 40
78	62	1.1	1	6 56
79	49	1.1	1	10 39
80	74	1.1	1	6 68
81	29	1.1	1	5 24
82	96	1.1	1	8 88
83	79	1.1	1	5 74
84	63	1.1	1	8 55
85	89	1.1	1	20 69
86	56	1.1	1	10 46
87	61	1.1	1	14 47
88	53	1.1	1	8 45
89	34	1.1	1	8 26
90	47	1.1	1	4 43
91	91	1.1	1	8 83
92	53	1.1	1	2 51
93	58	1.1	1	7 51
94	44	1.1	1	8 36
95	103	1.1	1	8 95
96	45	1.1	1	10 35
97	135	1.1	1	10 125
98	60	1.1	1	9 51
99	49	1.1	1	2 47
100	70	1.1	1	6 64


RUN STATISTICS FOR INPUT FILE: SRR3192399_2.fastq.gz
=============================================
76795926 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 76795926

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2461409 (3.21%)
