SUMMARISING RUN PARAMETERS
==========================
Input filename: R2.fastq
Trimming mode: paired-end
Trim Galore version: 0.4.0
Cutadapt version: 1.8.1
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
Length cut-off for read 1: 35 bp (default)
Length cut-off for read 2: 35 bp (default)


This is cutadapt 1.8.1 with Python 2.7.10
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC R2.fastq
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 2084.13 s (10 us/read; 5.79 M reads/minute).

=== Summary ===

Total reads processed:             200,998,380
Reads with adapters:                72,221,243 (35.9%)
Reads written (passing filters):   200,998,380 (100.0%)

Total basepairs processed: 15,275,876,880 bp
Quality-trimmed:             582,620,358 bp (3.8%)
Total written (filtered):  14,547,993,528 bp (95.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 72221243 times.

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

Bases preceding removed adapters:
  A: 34.2%
  C: 26.2%
  G: 17.6%
  T: 21.1%
  none/other: 0.9%

Overview of removed sequences
length	count	expect	max.err	error counts
1	53392369	50249595.0	0	53392369
2	12692989	12562398.8	0	12692989
3	3996044	3140599.7	0	3996044
4	898465	785149.9	0	898465
5	199957	196287.5	0	199957
6	41733	49071.9	0	41733
7	21420	12268.0	0	21420
8	16937	3067.0	0	16937
9	21594	766.7	0	15418 6176
10	21338	191.7	1	12772 8566
11	16835	47.9	1	11422 5413
12	12411	12.0	1	11193 1218
13	12316	3.0	1	9998 2318
14	13123	3.0	1	12314 809
15	7466	3.0	1	6846 620
16	8648	3.0	1	7523 1125
17	9515	3.0	1	9033 482
18	5625	3.0	1	5083 542
19	6811	3.0	1	6422 389
20	5214	3.0	1	4965 249
21	4196	3.0	1	3988 208
22	5056	3.0	1	4787 269
23	8323	3.0	1	5755 2568
24	7914	3.0	1	7268 646
25	6468	3.0	1	5960 508
26	10420	3.0	1	5889 4531
27	7100	3.0	1	6000 1100
28	7244	3.0	1	6611 633
29	5672	3.0	1	4854 818
30	12359	3.0	1	11824 535
31	2079	3.0	1	1623 456
32	3282	3.0	1	3072 210
33	2203	3.0	1	2014 189
34	2939	3.0	1	2686 253
35	3399	3.0	1	3149 250
36	3761	3.0	1	3478 283
37	3774	3.0	1	3480 294
38	3903	3.0	1	3569 334
39	4639	3.0	1	4278 361
40	5311	3.0	1	4954 357
41	6074	3.0	1	5422 652
42	11033	3.0	1	10481 552
43	3527	3.0	1	3210 317
44	5255	3.0	1	4529 726
45	7410	3.0	1	6983 427
46	2498	3.0	1	2316 182
47	3537	3.0	1	3265 272
48	2722	3.0	1	2518 204
49	3561	3.0	1	3277 284
50	7011	3.0	1	6634 377
51	5356	3.0	1	5029 327
52	2795	3.0	1	2571 224
53	2345	3.0	1	2117 228
54	4249	3.0	1	4023 226
55	5601	3.0	1	5243 358
56	4440	3.0	1	3896 544
57	5862	3.0	1	5432 430
58	12815	3.0	1	12283 532
59	9503	3.0	1	9079 424
60	11281	3.0	1	10794 487
61	16326	3.0	1	15494 832
62	30462	3.0	1	28919 1543
63	80723	3.0	1	77509 3214
64	147721	3.0	1	137737 9984
65	225595	3.0	1	207184 18411
66	68475	3.0	1	62667 5808
67	10044	3.0	1	8962 1082
68	3200	3.0	1	2861 339
69	1568	3.0	1	1362 206
70	912	3.0	1	808 104
71	836	3.0	1	580 256
72	571	3.0	1	458 113
73	787	3.0	1	415 372
74	613	3.0	1	495 118
75	1057	3.0	1	938 119
76	4626	3.0	1	4181 445


RUN STATISTICS FOR INPUT FILE: R2.fastq
=============================================
200998380 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 200998380

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5045367 (2.51%)