SUMMARISING RUN PARAMETERS
==========================
Input filename: KO-13006-2.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 KO-13006-2.end2.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 777.40 s (36 us/read; 1.69 M reads/minute).

=== Summary ===

Total reads processed:              21,881,230
Reads with adapters:                 8,639,944 (39.5%)
Reads written (passing filters):    21,881,230 (100.0%)

Total basepairs processed: 1,404,262,099 bp
Quality-trimmed:                  79,871 bp (0.0%)
Total written (filtered):  1,389,126,422 bp (98.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 8639944 times.

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

Bases preceding removed adapters:
  A: 27.2%
  C: 27.6%
  G: 23.4%
  T: 21.8%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	6764555	5470307.5	0	6764555
2	1271629	1367576.9	0	1271629
3	346479	341894.2	0	346479
4	75889	85473.6	0	75889
5	20220	21368.4	0	20220
6	11204	5342.1	0	11204
7	4108	1335.5	0	4108
8	3179	333.9	0	3179
9	3196	83.5	0	2546 650
10	3251	20.9	1	2171 1080
11	3805	5.2	1	2448 1357
12	3352	1.3	1	2474 878
13	3099	1.3	1	2523 576
14	3354	1.3	1	2278 1076
15	3190	1.3	1	2140 1050
16	2591	1.3	1	2015 576
17	2535	1.3	1	1981 554
18	2591	1.3	1	2366 225
19	3051	1.3	1	2662 389
20	3331	1.3	1	2897 434
21	3568	1.3	1	3270 298
22	4667	1.3	1	3717 950
23	5135	1.3	1	4791 344
24	5042	1.3	1	4665 377
25	3655	1.3	1	3402 253
26	3115	1.3	1	2826 289
27	3052	1.3	1	2652 400
28	3469	1.3	1	3117 352
29	3920	1.3	1	3610 310
30	4402	1.3	1	4120 282
31	4569	1.3	1	4249 320
32	4996	1.3	1	4675 321
33	8776	1.3	1	8304 472
34	3971	1.3	1	3660 311
35	7269	1.3	1	6922 347
36	3746	1.3	1	3444 302
37	3694	1.3	1	3487 207
38	6059	1.3	1	5675 384
39	1881	1.3	1	1673 208
40	2824	1.3	1	2577 247
41	1426	1.3	1	1198 228
42	870	1.3	1	716 154
43	961	1.3	1	510 451
44	515	1.3	1	340 175
45	686	1.3	1	358 328
46	594	1.3	1	383 211
47	491	1.3	1	312 179
48	853	1.3	1	545 308
49	949	1.3	1	771 178
50	1566	1.3	1	84 1482
51	305	1.3	1	14 291
52	222	1.3	1	11 211
53	476	1.3	1	3 473
54	117	1.3	1	11 106
55	412	1.3	1	2 410
56	195	1.3	1	10 185
57	163	1.3	1	5 158
58	376	1.3	1	4 372
59	239	1.3	1	3 236
60	1024	1.3	1	3 1021
61	173	1.3	1	7 166
62	242	1.3	1	41 201
63	407	1.3	1	4 403
64	140	1.3	1	16 124
65	139	1.3	1	6 133
66	146	1.3	1	3 143
67	191	1.3	1	4 187
68	356	1.3	1	7 349
69	85	1.3	1	4 81
70	90	1.3	1	11 79
71	47	1.3	1	5 42
72	77	1.3	1	10 67
73	411	1.3	1	22 389
74	141	1.3	1	56 85
75	2362	1.3	1	2118 244
76	78	1.3	1	8 70


RUN STATISTICS FOR INPUT FILE: KO-13006-2.end2.fastq.gz
=============================================
21881230 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 21881230

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 19588 (0.09%)