SUMMARISING RUN PARAMETERS ========================== Input filename: SRR546474_1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 3595). Second best hit was Nextera (count: 0) 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 Output file will be GZIP compressed This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR546474_1.fastq.gz Processing single-end reads on 1 core ... Finished in 2208.885 s (28.607 µs/read; 2.10 M reads/minute). === Summary === Total reads processed: 77,213,856 Reads with adapters: 28,454,187 (36.9%) Reads written (passing filters): 77,213,856 (100.0%) Total basepairs processed: 6,949,247,040 bp Quality-trimmed: 127,853,587 bp (1.8%) Total written (filtered): 6,776,563,810 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 28454187 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.0% C: 0.1% G: 13.5% T: 48.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22358587 19303464.0 0 22358587 2 3785932 4825866.0 0 3785932 3 1281777 1206466.5 0 1281777 4 603243 301616.6 0 603243 5 21591 75404.2 0 21591 6 17273 18851.0 0 17273 7 15466 4712.8 0 15466 8 15054 1178.2 0 15054 9 17500 294.5 0 16774 726 10 16953 73.6 1 15422 1531 11 14874 18.4 1 14311 563 12 12863 4.6 1 12482 381 13 12625 1.2 1 12247 378 14 12721 1.2 1 12270 451 15 13543 1.2 1 13089 454 16 12592 1.2 1 12062 530 17 16267 1.2 1 15681 586 18 12865 1.2 1 12386 479 19 14223 1.2 1 13711 512 20 11520 1.2 1 11087 433 21 11268 1.2 1 10875 393 22 12347 1.2 1 11950 397 23 10227 1.2 1 9920 307 24 10219 1.2 1 9908 311 25 9180 1.2 1 8845 335 26 12034 1.2 1 11656 378 27 11500 1.2 1 11183 317 28 8219 1.2 1 7967 252 29 7489 1.2 1 7272 217 30 8575 1.2 1 8342 233 31 7689 1.2 1 7452 237 32 6907 1.2 1 6737 170 33 6653 1.2 1 6458 195 34 6198 1.2 1 6036 162 35 6187 1.2 1 6003 184 36 8365 1.2 1 8164 201 37 6606 1.2 1 6430 176 38 6364 1.2 1 6188 176 39 6831 1.2 1 6711 120 40 2082 1.2 1 2004 78 41 3069 1.2 1 2997 72 42 2515 1.2 1 2456 59 43 2000 1.2 1 1947 53 44 1856 1.2 1 1805 51 45 1999 1.2 1 1955 44 46 1973 1.2 1 1924 49 47 1052 1.2 1 1019 33 48 1099 1.2 1 1071 28 49 1088 1.2 1 1062 26 50 882 1.2 1 864 18 51 709 1.2 1 686 23 52 684 1.2 1 669 15 53 618 1.2 1 602 16 54 700 1.2 1 686 14 55 449 1.2 1 441 8 56 399 1.2 1 389 10 57 120 1.2 1 118 2 58 117 1.2 1 111 6 59 94 1.2 1 90 4 60 141 1.2 1 137 4 61 33 1.2 1 33 62 17 1.2 1 16 1 63 25 1.2 1 22 3 64 24 1.2 1 24 65 28 1.2 1 26 2 66 38 1.2 1 38 67 20 1.2 1 18 2 68 2 1.2 1 0 2 70 1 1.2 1 0 1 71 9 1.2 1 6 3 76 2 1.2 1 0 2 81 1 1.2 1 0 1 82 2 1.2 1 0 2 84 1 1.2 1 0 1 85 2 1.2 1 0 2 86 1 1.2 1 0 1 88 1 1.2 1 0 1 90 7 1.2 1 0 7 RUN STATISTICS FOR INPUT FILE: SRR546474_1.fastq.gz ============================================= 77213856 sequences processed in total