SUMMARISING RUN PARAMETERS ========================== Input filename: Geo_Pool_M_CTTGTA_L006_R1_001.fastq Trimming mode: single-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 before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed 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 Geo_Pool_M_CTTGTA_L006_R1_001.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1226.22 s (10 us/read; 5.76 M reads/minute). === Summary === Total reads processed: 117,663,240 Reads with adapters: 36,573,174 (31.1%) Reads written (passing filters): 117,663,240 (100.0%) Total basepairs processed: 11,883,987,240 bp Quality-trimmed: 93,468,521 bp (0.8%) Total written (filtered): 11,719,003,078 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36573174 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.2% C: 27.7% G: 22.0% T: 20.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 25314985 29415810.0 0 25314985 2 7083781 7353952.5 0 7083781 3 2055289 1838488.1 0 2055289 4 528362 459622.0 0 528362 5 168427 114905.5 0 168427 6 141699 28726.4 0 141699 7 126831 7181.6 0 126831 8 103210 1795.4 0 103210 9 103800 448.8 0 102998 802 10 97754 112.2 1 95922 1832 11 73805 28.1 1 72519 1286 12 80967 7.0 1 79627 1340 13 60342 1.8 1 59215 1127 14 59644 1.8 1 58560 1084 15 52364 1.8 1 51290 1074 16 45994 1.8 1 44529 1465 17 43596 1.8 1 42339 1257 18 49349 1.8 1 47755 1594 19 30364 1.8 1 29445 919 20 35193 1.8 1 34163 1030 21 29228 1.8 1 28373 855 22 29103 1.8 1 28224 879 23 23037 1.8 1 22244 793 24 21212 1.8 1 20357 855 25 17349 1.8 1 16828 521 26 16326 1.8 1 15741 585 27 15511 1.8 1 14971 540 28 15182 1.8 1 14584 598 29 11906 1.8 1 11596 310 30 11697 1.8 1 11371 326 31 7589 1.8 1 7364 225 32 9443 1.8 1 9211 232 33 7108 1.8 1 6940 168 34 7346 1.8 1 7143 203 35 6915 1.8 1 6724 191 36 5646 1.8 1 5486 160 37 5643 1.8 1 5479 164 38 5219 1.8 1 5075 144 39 4201 1.8 1 4068 133 40 4217 1.8 1 4081 136 41 4405 1.8 1 4263 142 42 3254 1.8 1 3168 86 43 2637 1.8 1 2572 65 44 2372 1.8 1 2276 96 45 2682 1.8 1 2571 111 46 2483 1.8 1 2356 127 47 1993 1.8 1 1905 88 48 1877 1.8 1 1819 58 49 1900 1.8 1 1828 72 50 1600 1.8 1 1527 73 51 1565 1.8 1 1479 86 52 1652 1.8 1 1535 117 53 1577 1.8 1 1515 62 54 951 1.8 1 900 51 55 1053 1.8 1 980 73 56 974 1.8 1 902 72 57 1060 1.8 1 989 71 58 943 1.8 1 843 100 59 1061 1.8 1 983 78 60 764 1.8 1 652 112 61 815 1.8 1 728 87 62 819 1.8 1 642 177 63 1077 1.8 1 798 279 64 883 1.8 1 704 179 65 606 1.8 1 444 162 66 715 1.8 1 487 228 67 939 1.8 1 560 379 68 1163 1.8 1 513 650 69 3967 1.8 1 565 3402 70 3654 1.8 1 959 2695 71 3086 1.8 1 630 2456 72 1986 1.8 1 362 1624 73 1579 1.8 1 207 1372 74 1220 1.8 1 129 1091 75 300 1.8 1 76 224 76 250 1.8 1 31 219 77 211 1.8 1 17 194 78 154 1.8 1 19 135 79 133 1.8 1 18 115 80 81 1.8 1 15 66 81 59 1.8 1 7 52 82 75 1.8 1 5 70 83 87 1.8 1 11 76 84 49 1.8 1 15 34 85 31 1.8 1 6 25 86 21 1.8 1 5 16 87 29 1.8 1 4 25 88 31 1.8 1 8 23 89 25 1.8 1 7 18 90 18 1.8 1 6 12 91 44 1.8 1 6 38 92 12 1.8 1 4 8 93 27 1.8 1 1 26 94 24 1.8 1 0 24 95 30 1.8 1 2 28 96 65 1.8 1 2 63 97 57 1.8 1 2 55 98 121 1.8 1 4 117 99 182 1.8 1 5 177 100 494 1.8 1 0 494 101 1618 1.8 1 1 1617 RUN STATISTICS FOR INPUT FILE: Geo_Pool_M_CTTGTA_L006_R1_001.fastq ============================================= 117663240 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 54665 (0.0%)