SUMMARISING RUN PARAMETERS
==========================
Input filename: A-15173-1.end2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.16
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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
All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1
Output file will be GZIP compressed


This is cutadapt 1.16 with Python 2.7.13
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA A-15173-1.end2.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1141.83 s (37 us/read; 1.61 M reads/minute).

=== Summary ===

Total reads processed:              30,709,434
Reads with adapters:                11,945,386 (38.9%)
Reads written (passing filters):    30,709,434 (100.0%)

Total basepairs processed: 1,981,525,061 bp
Quality-trimmed:                  66,959 bp (0.0%)
Total written (filtered):  1,962,380,561 bp (99.0%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 11945386 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 27.7%
  C: 27.3%
  G: 23.1%
  T: 21.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9380453	7677358.5	0	9380453
2	1792977	1919339.6	0	1792977
3	478936	479834.9	0	478936
4	105287	119958.7	0	105287
5	26687	29989.7	0	26687
6	14753	7497.4	0	14753
7	4985	1874.4	0	4985
8	3632	468.6	0	3632
9	3711	117.1	0	2701 1010
10	3698	29.3	1	2176 1522
11	4213	7.3	1	2276 1937
12	3593	1.8	1	2498 1095
13	3265	1.8	1	2449 816
14	3887	1.8	1	2147 1740
15	3609	1.8	1	1927 1682
16	2731	1.8	1	1878 853
17	2662	1.8	1	1915 747
18	2394	1.8	1	2077 317
19	2986	1.8	1	2471 515
20	3223	1.8	1	2644 579
21	3498	1.8	1	3138 360
22	5015	1.8	1	3661 1354
23	5297	1.8	1	4862 435
24	5285	1.8	1	4762 523
25	3607	1.8	1	3319 288
26	2873	1.8	1	2451 422
27	2892	1.8	1	2398 494
28	3154	1.8	1	2702 452
29	3515	1.8	1	3100 415
30	3916	1.8	1	3592 324
31	4162	1.8	1	3819 343
32	4273	1.8	1	3976 297
33	8230	1.8	1	7696 534
34	3665	1.8	1	3337 328
35	6166	1.8	1	5797 369
36	3033	1.8	1	2694 339
37	2711	1.8	1	2456 255
38	4350	1.8	1	3943 407
39	1379	1.8	1	1116 263
40	1894	1.8	1	1600 294
41	945	1.8	1	694 251
42	613	1.8	1	434 179
43	986	1.8	1	316 670
44	516	1.8	1	263 253
45	767	1.8	1	248 519
46	587	1.8	1	245 342
47	417	1.8	1	180 237
48	821	1.8	1	337 484
49	738	1.8	1	465 273
50	2307	1.8	1	49 2258
51	421	1.8	1	13 408
52	345	1.8	1	7 338
53	646	1.8	1	4 642
54	160	1.8	1	0 160
55	591	1.8	1	5 586
56	322	1.8	1	2 320
57	218	1.8	1	4 214
58	565	1.8	1	0 565
59	368	1.8	1	4 364
60	1345	1.8	1	2 1343
61	182	1.8	1	5 177
62	276	1.8	1	14 262
63	559	1.8	1	4 555
64	156	1.8	1	4 152
65	154	1.8	1	7 147
66	208	1.8	1	0 208
67	283	1.8	1	6 277
68	587	1.8	1	2 585
69	110	1.8	1	7 103
70	109	1.8	1	6 103
71	72	1.8	1	6 66
72	127	1.8	1	11 116
73	564	1.8	1	18 546
74	174	1.8	1	37 137
75	1462	1.8	1	1191 271
76	88	1.8	1	15 73


RUN STATISTICS FOR INPUT FILE: A-15173-1.end2.fastq.gz
=============================================
30709434 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 30709434

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 24808 (0.08%)