test_data

src/multiqc/test_data/rna-seq/data/SRR3192396_1.fastq.gz_trimming_report.txt

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+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: SRR3192396_1.fastq.gz
+Trimming mode: paired-end
+Trim Galore version: 0.4.1
+Cutadapt version: 1.9.1
+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
+Running FastQC on the data once trimming has completed
+Output file will be GZIP compressed
+
+
+This is cutadapt 1.9.1 with Python 2.7.6
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192396_1.fastq.gz
+Trimming 1 adapter with at most 10.0% errors in single-end mode ...
+Finished in 2200.70 s (21 us/read; 2.87 M reads/minute).
+
+=== Summary ===
+
+Total reads processed:             105,089,150
+Reads with adapters:                31,907,642 (30.4%)
+Reads written (passing filters):   105,089,150 (100.0%)
+
+Total basepairs processed: 10,614,004,150 bp
+Quality-trimmed:             223,928,038 bp (2.1%)
+Total written (filtered):  10,345,268,814 bp (97.5%)
+
+=== Adapter 1 ===
+
+Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 31907642 times.
+
+No. of allowed errors:
+0-9 bp: 0; 10-13 bp: 1
+
+Bases preceding removed adapters:
+  A: 29.0%
+  C: 30.8%
+  G: 18.8%
+  T: 21.4%
+  none/other: 0.0%
+
+Overview of removed sequences
+length	count	expect	max.err	error counts
+1	22534133	26272287.5	0	22534133
+2	7424483	6568071.9	0	7424483
+3	1447916	1642018.0	0	1447916
+4	343385	410504.5	0	343385
+5	88652	102626.1	0	88652
+6	13787	25656.5	0	13787
+7	3613	6414.1	0	3613
+8	2961	1603.5	0	2961
+9	3515	400.9	0	2662 853
+10	4242	100.2	1	2597 1645
+11	3413	25.1	1	2440 973
+12	2534	6.3	1	2396 138
+13	2448	1.6	1	2395 53
+14	2629	1.6	1	2583 46
+15	2103	1.6	1	2054 49
+16	1982	1.6	1	1930 52
+17	1694	1.6	1	1620 74
+18	1618	1.6	1	1568 50
+19	895	1.6	1	861 34
+20	1097	1.6	1	1054 43
+21	873	1.6	1	848 25
+22	864	1.6	1	826 38
+23	1038	1.6	1	974 64
+24	918	1.6	1	857 61
+25	747	1.6	1	723 24
+26	628	1.6	1	590 38
+27	789	1.6	1	743 46
+28	793	1.6	1	749 44
+29	881	1.6	1	840 41
+30	878	1.6	1	834 44
+31	848	1.6	1	785 63
+32	774	1.6	1	731 43
+33	1003	1.6	1	965 38
+34	769	1.6	1	733 36
+35	993	1.6	1	934 59
+36	688	1.6	1	646 42
+37	891	1.6	1	843 48
+38	470	1.6	1	432 38
+39	572	1.6	1	541 31
+40	416	1.6	1	370 46
+41	505	1.6	1	477 28
+42	222	1.6	1	176 46
+43	196	1.6	1	173 23
+44	138	1.6	1	94 44
+45	216	1.6	1	185 31
+46	193	1.6	1	157 36
+47	130	1.6	1	88 42
+48	153	1.6	1	101 52
+49	126	1.6	1	95 31
+50	87	1.6	1	69 18
+51	81	1.6	1	49 32
+52	118	1.6	1	73 45
+53	79	1.6	1	51 28
+54	47	1.6	1	17 30
+55	60	1.6	1	19 41
+56	71	1.6	1	46 25
+57	55	1.6	1	29 26
+58	63	1.6	1	33 30
+59	42	1.6	1	28 14
+60	50	1.6	1	12 38
+61	49	1.6	1	26 23
+62	74	1.6	1	39 35
+63	74	1.6	1	52 22
+64	58	1.6	1	41 17
+65	74	1.6	1	40 34
+66	65	1.6	1	34 31
+67	83	1.6	1	41 42
+68	49	1.6	1	33 16
+69	92	1.6	1	62 30
+70	105	1.6	1	52 53
+71	63	1.6	1	39 24
+72	50	1.6	1	16 34
+73	37	1.6	1	5 32
+74	37	1.6	1	4 33
+75	27	1.6	1	3 24
+76	32	1.6	1	2 30
+77	20	1.6	1	0 20
+78	52	1.6	1	0 52
+79	29	1.6	1	1 28
+80	38	1.6	1	0 38
+81	59	1.6	1	2 57
+82	59	1.6	1	0 59
+83	40	1.6	1	0 40
+84	35	1.6	1	0 35
+85	33	1.6	1	0 33
+86	56	1.6	1	0 56
+87	66	1.6	1	0 66
+88	39	1.6	1	0 39
+89	51	1.6	1	0 51
+90	54	1.6	1	0 54
+91	30	1.6	1	0 30
+92	40	1.6	1	0 40
+93	14	1.6	1	0 14
+94	133	1.6	1	1 132
+95	45	1.6	1	0 45
+96	31	1.6	1	0 31
+97	56	1.6	1	0 56
+98	30	1.6	1	0 30
+99	9	1.6	1	0 9
+100	21	1.6	1	0 21
+101	68	1.6	1	0 68
+
+
+RUN STATISTICS FOR INPUT FILE: SRR3192396_1.fastq.gz
+=============================================
+105089150 sequences processed in total
+

src/multiqc/test_data/rna-seq/data/SRR3192396_1Log.final.out

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+                                 Started job on |	May 03 04:15:10
+                             Started mapping on |	May 03 04:19:43
+                                    Finished on |	May 03 05:44:43
+       Mapping speed, Million of reads per hour |	73.70
+
+                          Number of input reads |	104413184
+                      Average input read length |	196
+                                    UNIQUE READS:
+                   Uniquely mapped reads number |	97833503
+                        Uniquely mapped reads % |	93.70%
+                          Average mapped length |	195.57
+                       Number of splices: Total |	40714338
+            Number of splices: Annotated (sjdb) |	40114995
+                       Number of splices: GT/AG |	40194421
+                       Number of splices: GC/AG |	336796
+                       Number of splices: AT/AC |	41871
+               Number of splices: Non-canonical |	141250
+                      Mismatch rate per base, % |	0.25%
+                         Deletion rate per base |	0.02%
+                        Deletion average length |	1.56
+                        Insertion rate per base |	0.01%
+                       Insertion average length |	1.61
+                             MULTI-MAPPING READS:
+        Number of reads mapped to multiple loci |	3659822
+             % of reads mapped to multiple loci |	3.51%
+        Number of reads mapped to too many loci |	11548
+             % of reads mapped to too many loci |	0.01%
+                                  UNMAPPED READS:
+       % of reads unmapped: too many mismatches |	0.00%
+                 % of reads unmapped: too short |	2.77%
+                     % of reads unmapped: other |	0.02%
+                                  CHIMERIC READS:
+                       Number of chimeric reads |	0
+                            % of chimeric reads |	0.00%