{
  "tool": "Trim Galore",
  "schema_version": 1,
  "trim_galore_version": "2.3.0",
  "input_filenames": ["SRR6995994.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/SRR6995994.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": 9188940,
    "reads_with_adapter": 7714396,
    "reads_written": 4198697,
    "reads_too_short": 4990243,
    "reads_too_long": 0,
    "reads_too_many_n": 0,
    "reads_discarded_untrimmed": 0
  },
  "basepair_processing": {
    "total_bp_processed": 928082940,
    "quality_trimmed_bp": 208253890,
    "total_bp_written": 344978925
  },
  "adapter_trimming": [
    {
      "name": "Illumina",
      "sequence": "AGATCGGAAGAGC",
      "type": "regular 3'",
      "length": 13,
      "times_trimmed": 7714396,
      "length_distribution": {
        "1": 1492673,
        "2": 128606,
        "3": 46575,
        "4": 41159,
        "5": 37536,
        "6": 41569,
        "7": 48187,
        "8": 28646,
        "9": 34008,
        "10": 40831,
        "11": 21065,
        "12": 38704,
        "13": 27571,
        "14": 29986,
        "15": 30811,
        "16": 33796,
        "17": 31481,
        "18": 36540,
        "19": 16404,
        "20": 27251,
        "21": 27037,
        "22": 29373,
        "23": 20042,
        "24": 23565,
        "25": 26835,
        "26": 20970,
        "27": 24430,
        "28": 29629,
        "29": 20776,
        "30": 26214,
        "31": 11647,
        "32": 24787,
        "33": 19825,
        "34": 22065,
        "35": 17506,
        "36": 19797,
        "37": 16920,
        "38": 14304,
        "39": 26209,
        "40": 19198,
        "41": 20520,
        "42": 18071,
        "43": 14907,
        "44": 16886,
        "45": 15612,
        "46": 12394,
        "47": 10591,
        "48": 9609,
        "49": 9522,
        "50": 9294,
        "51": 13903,
        "52": 13239,
        "53": 8979,
        "54": 9200,
        "55": 8072,
        "56": 12312,
        "57": 16342,
        "58": 16992,
        "59": 9771,
        "60": 15041,
        "61": 18860,
        "62": 60094,
        "63": 81473,
        "64": 21614,
        "65": 27266,
        "66": 62431,
        "67": 216122,
        "68": 512942,
        "69": 1759487,
        "70": 1030923,
        "71": 385489,
        "72": 136008,
        "73": 37320,
        "74": 18790,
        "75": 10622,
        "76": 8751,
        "77": 11809,
        "78": 11503,
        "79": 10575,
        "80": 9203,
        "81": 8005,
        "82": 7640,
        "83": 6731,
        "84": 6624,
        "85": 6531,
        "86": 6911,
        "87": 7263,
        "88": 6993,
        "89": 7121,
        "90": 7430,
        "91": 7861,
        "92": 8386,
        "93": 8863,
        "94": 9659,
        "95": 10322,
        "96": 11715,
        "97": 13349,
        "98": 14698,
        "99": 16886,
        "100": 33928,
        "101": 140413
      }
    }
  ],
  "poly_a_trimming": {
    "reads_trimmed": 0,
    "bases_removed": 0
  },
  "poly_g_trimming": {
    "reads_trimmed": 103008,
    "bases_removed": 441874
  },
  "rrbs": {
    "trimmed_3prime": 0,
    "trimmed_5prime": 0,
    "r2_clipped_5prime": 0
  },
  "pair_validation": null,
  "passthrough": null
}
