{
  "tool": "Trim Galore",
  "schema_version": 1,
  "trim_galore_version": "2.3.0",
  "input_filenames": ["SRR6995993.fastq.gz"],
  "mode": "single-end",
  "read_number": 1,
  "command_line": "trim_galore --cores 20 --quality 20 --length 20 --fastqc --fastqc_args --outdir ../output/02-qc-trim/fastqc-trimmed --output_dir ../data/trimmed-reads ../data/raw-reads/SRR6995993.fastq.gz",
  "parameters": {
    "quality_cutoff": 20,
    "adapters": [{"name": "Illumina", "sequence": "AGATCGGAAGAGC"}],
    "adapters_r2": [],
    "times": 1,
    "error_rate": 0.1,
    "stringency": 1,
    "length_cutoff": 20,
    "max_length": null,
    "phred_encoding": 33,
    "trim_n": false,
    "nextseq": false,
    "rrbs": false,
    "non_directional": false,
    "poly_a": false,
    "poly_g": true,
    "clip_r1": null,
    "clip_r2": null,
    "three_prime_clip_r1": null,
    "three_prime_clip_r2": null,
    "max_n": null,
    "discard_untrimmed": false,
    "consider_already_trimmed": null
  },
  "read_processing": {
    "total_reads": 25752634,
    "reads_with_adapter": 15393563,
    "reads_written": 22511513,
    "reads_too_short": 3241121,
    "reads_too_long": 0,
    "reads_too_many_n": 0,
    "reads_discarded_untrimmed": 0
  },
  "basepair_processing": {
    "total_bp_processed": 2601016034,
    "quality_trimmed_bp": 168252428,
    "total_bp_written": 2138630058
  },
  "adapter_trimming": [
    {
      "name": "Illumina",
      "sequence": "AGATCGGAAGAGC",
      "type": "regular 3'",
      "length": 13,
      "times_trimmed": 15393563,
      "length_distribution": {
        "1": 7645997,
        "2": 534343,
        "3": 291109,
        "4": 245902,
        "5": 222809,
        "6": 221201,
        "7": 227983,
        "8": 176189,
        "9": 191705,
        "10": 196403,
        "11": 135410,
        "12": 172032,
        "13": 142443,
        "14": 139453,
        "15": 140261,
        "16": 127613,
        "17": 141045,
        "18": 145508,
        "19": 61757,
        "20": 97023,
        "21": 90106,
        "22": 85550,
        "23": 72642,
        "24": 72920,
        "25": 65492,
        "26": 57563,
        "27": 54733,
        "28": 59928,
        "29": 41393,
        "30": 49108,
        "31": 23838,
        "32": 37226,
        "33": 26212,
        "34": 29751,
        "35": 22545,
        "36": 23175,
        "37": 18672,
        "38": 16053,
        "39": 13969,
        "40": 11682,
        "41": 10476,
        "42": 10739,
        "43": 8515,
        "44": 7287,
        "45": 6867,
        "46": 6170,
        "47": 4626,
        "48": 4038,
        "49": 4377,
        "50": 4703,
        "51": 5286,
        "52": 5055,
        "53": 3891,
        "54": 3728,
        "55": 3839,
        "56": 4944,
        "57": 7121,
        "58": 7219,
        "59": 5116,
        "60": 7817,
        "61": 10532,
        "62": 26665,
        "63": 53960,
        "64": 17759,
        "65": 22284,
        "66": 49172,
        "67": 173170,
        "68": 380144,
        "69": 1270585,
        "70": 552214,
        "71": 201199,
        "72": 72347,
        "73": 21280,
        "74": 11117,
        "75": 6492,
        "76": 5119,
        "77": 6705,
        "78": 6642,
        "79": 6064,
        "80": 5659,
        "81": 5193,
        "82": 4999,
        "83": 4639,
        "84": 4373,
        "85": 4621,
        "86": 4757,
        "87": 5135,
        "88": 4925,
        "89": 4758,
        "90": 5314,
        "91": 5626,
        "92": 5942,
        "93": 6196,
        "94": 6672,
        "95": 7356,
        "96": 8416,
        "97": 9216,
        "98": 10374,
        "99": 11835,
        "100": 23941,
        "101": 99608
      }
    }
  ],
  "poly_a_trimming": {
    "reads_trimmed": 0,
    "bases_removed": 0
  },
  "poly_g_trimming": {
    "reads_trimmed": 287752,
    "bases_removed": 1190135
  },
  "rrbs": {
    "trimmed_3prime": 0,
    "trimmed_5prime": 0,
    "r2_clipped_5prime": 0
  },
  "pair_validation": null,
  "passthrough": null
}
