SUMMARISING RUN PARAMETERS
==========================
Input filename: ENCFF001HPF.fastq.gz
Trimming mode: single-end
Trim Galore version: 0.4.1
Cutadapt version: 1.10
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 before a sequence gets removed: 20 bp
Output file will be GZIP compressed


This is cutadapt 1.10 with Python 2.7.5
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ENCFF001HPF.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 448.70 s (25 us/read; 2.43 M reads/minute).

=== Summary ===

Total reads processed:              18,165,721
Reads with adapters:                 5,374,101 (29.6%)
Reads written (passing filters):    18,165,721 (100.0%)

Total basepairs processed:   653,965,956 bp
Quality-trimmed:             263,605,688 bp (40.3%)
Total written (filtered):    382,866,367 bp (58.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5374101 times.

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

Bases preceding removed adapters:
  A: 33.0%
  C: 23.0%
  G: 14.4%
  T: 20.5%
  none/other: 9.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	3931319	4541430.2	0	3931319
2	1113397	1135357.6	0	1113397
3	226070	283839.4	0	226070
4	76340	70959.8	0	76340
5	6104	17740.0	0	6104
6	2134	4435.0	0	2134
7	784	1108.7	0	784
8	578	277.2	0	578
9	2452	69.3	0	497 1955
10	1002	17.3	1	355 647
11	2250	4.3	1	141 2109
12	826	1.1	1	194 632
13	724	0.3	1	27 697
14	476	0.3	1	182 294
15	2064	0.3	1	8 2056
16	470	0.3	1	40 430
17	258	0.3	1	9 249
18	742	0.3	1	9 733
19	1045	0.3	1	28 1017
20	234	0.3	1	6 228
21	120	0.3	1	0 120
22	992	0.3	1	0 992
23	151	0.3	1	2 149
24	31	0.3	1	1 30
25	206	0.3	1	0 206
26	782	0.3	1	0 782
27	61	0.3	1	2 59
28	463	0.3	1	0 463
29	83	0.3	1	0 83
30	19	0.3	1	0 19
31	104	0.3	1	0 104
32	1230	0.3	1	0 1230
33	45	0.3	1	0 45
34	14	0.3	1	0 14
35	93	0.3	1	0 93
36	438	0.3	1	1 437


RUN STATISTICS FOR INPUT FILE: ENCFF001HPF.fastq.gz
=============================================
18165721 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	7611341 (41.9%)