SUMMARISING RUN PARAMETERS
==========================
Input filename: KO-N4371-1.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 KO-N4371-1.end2.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1078.08 s (35 us/read; 1.69 M reads/minute).

=== Summary ===

Total reads processed:              30,394,942
Reads with adapters:                12,551,375 (41.3%)
Reads written (passing filters):    30,394,942 (100.0%)

Total basepairs processed: 1,999,712,331 bp
Quality-trimmed:               2,638,711 bp (0.1%)
Total written (filtered):  1,949,595,023 bp (97.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 12551375 times.

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

Bases preceding removed adapters:
  A: 25.5%
  C: 28.0%
  G: 23.5%
  T: 22.3%
  none/other: 0.6%

Overview of removed sequences
length	count	expect	max.err	error counts
1	8888912	7598735.5	0	8888912
2	1777319	1899683.9	0	1777319
3	512833	474921.0	0	512833
4	127103	118730.2	0	127103
5	46304	29682.6	0	46304
6	27243	7420.6	0	27243
7	20079	1855.2	0	20079
8	17872	463.8	0	17872
9	22478	115.9	0	21501 977
10	25937	29.0	1	18491 7446
11	30287	7.2	1	21817 8470
12	29454	1.8	1	21444 8010
13	29477	1.8	1	21752 7725
14	24413	1.8	1	17568 6845
15	28336	1.8	1	20290 8046
16	20108	1.8	1	14637 5471
17	21238	1.8	1	14465 6773
18	20897	1.8	1	15391 5506
19	29595	1.8	1	20393 9202
20	21946	1.8	1	14561 7385
21	27268	1.8	1	16971 10297
22	33086	1.8	1	16288 16798
23	32701	1.8	1	17156 15545
24	38985	1.8	1	18836 20149
25	38283	1.8	1	16812 21471
26	26863	1.8	1	12200 14663
27	24385	1.8	1	10199 14186
28	29445	1.8	1	12460 16985
29	29878	1.8	1	13227 16651
30	34882	1.8	1	15733 19149
31	46134	1.8	1	21521 24613
32	49721	1.8	1	33127 16594
33	64210	1.8	1	41709 22501
34	29057	1.8	1	18877 10180
35	68755	1.8	1	45040 23715
36	36991	1.8	1	25987 11004
37	31154	1.8	1	21200 9954
38	45524	1.8	1	31215 14309
39	17041	1.8	1	11864 5177
40	31447	1.8	1	22292 9155
41	15351	1.8	1	10663 4688
42	7923	1.8	1	4658 3265
43	6445	1.8	1	3574 2871
44	2982	1.8	1	1788 1194
45	3555	1.8	1	2180 1375
46	3146	1.8	1	1997 1149
47	2235	1.8	1	1394 841
48	2798	1.8	1	1697 1101
49	3447	1.8	1	2283 1164
50	5211	1.8	1	2366 2845
51	846	1.8	1	321 525
52	588	1.8	1	215 373
53	789	1.8	1	133 656
54	358	1.8	1	129 229
55	735	1.8	1	142 593
56	491	1.8	1	175 316
57	246	1.8	1	52 194
58	581	1.8	1	54 527
59	374	1.8	1	59 315
60	1302	1.8	1	51 1251
61	311	1.8	1	67 244
62	531	1.8	1	225 306
63	974	1.8	1	383 591
64	270	1.8	1	105 165
65	303	1.8	1	99 204
66	307	1.8	1	68 239
67	439	1.8	1	97 342
68	659	1.8	1	106 553
69	266	1.8	1	117 149
70	386	1.8	1	186 200
71	370	1.8	1	215 155
72	487	1.8	1	264 223
73	1126	1.8	1	465 661
74	949	1.8	1	663 286
75	6641	1.8	1	5586 1055
76	20312	1.8	1	15041 5271


RUN STATISTICS FOR INPUT FILE: KO-N4371-1.end2.fastq.gz
=============================================
30394942 sequences processed in total
TTotal number of sequences analysed for the sequence pair length validation: 30394942

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 63455 (0.21%)