{
  "source_table": "methylation_level.txt",
  "source_column": "Methylation_level_CG",
  "source_sha256": "95a7fbfd8feec8a365c25c19e7d6d8e501846eb52642b8e55b9627fe83986411",
  "source_file_url": "https://www.mapleomics.com/data/wgbs_delivered_methylation_level.tsv",
  "mapping_file_url": "https://www.mapleomics.com/data/wgbs_reported_cg.tsv?v=20260905sources1",
  "checked_utc": "2026-09-06T04:49:41Z",
  "status": "The original-delivery table is retained as a separate source. Active website summaries and coverage tracks follow the processing described in website_summary and website_bigwig.",
  "source_project": "PRJNA1163018",
  "source_project_url": "https://www.ebi.ac.uk/ena/browser/view/PRJNA1163018",
  "analysis_report": {
    "name": "WGBS_report.html (2024-08-08 analysis report)",
    "sha256": "ffe24552eb696073db5c9f002409060f657ba6136f7f5e5f086bf7261b99ac35",
    "method_sections": [
      "4.2 C-site sequencing depth and coverage",
      "5.1 Methylation site calling",
      "5.2 M-bias assessment"
    ],
    "methylation_formula": "methylated reads / (methylated reads + unmethylated reads)",
    "cross_site_aggregation": "Not specified: pooled read counts versus arithmetic mean of site fractions cannot be distinguished from the report.",
    "depth_filter": "Report text states depth >5; coverage table labels use depth >=5. The exact implemented boundary has not been verified.",
    "paired_read_overlap": "The report states no_overlap was used, retaining read 1 information in overlapping paired-end reads.",
    "read_end_filter": "The report describes ignoring the first 5 bp in methylation calling when not already trimmed; its parameter table lists -ignore 5 --ignore_r2 5.",
    "execution_status": "Reported methods; no independent read-level recomputation or execution-log validation."
  },
  "website_bigwig": {
    "signal": "RPKM-normalized read coverage",
    "bin_size_bp": 10,
    "input": "coordinate-sorted, Bismark-deduplicated paired-end BAM",
    "command": "bamCoverage -b <deduplicated.bam> -o <sample.bw> --normalizeUsing RPKM --binSize 10 -p 12",
    "generation_script": "fix_wgbs_v2.sh",
    "generation_script_sha256": "020954bbcc46c925485e250a526efeae8cf06728f0f841e6046671b7cae92f60",
    "generation_evidence": "Successful sample logs and SHA-256 identity of all nine served BigWig files with the processing outputs.",
    "original_delivery_tracks": "The 27 CG/CHG/CHH BigWigs in the original delivery are a separate track set."
  },
  "website_summary": {
    "source_table": "wgbs_methylation_summary.tsv",
    "source_file_url": "https://www.mapleomics.com/data/wgbs_methylation_summary.tsv",
    "source_sha256": "53d9d2552dbc7db3b7d87280b5951a42b04c80f83f0c449f531892742d806977",
    "source_project": "PRJNA1163018",
    "biological_samples": 9,
    "libraries": {
      "ATAC-seq": 9,
      "WGBS": 9
    },
    "biosamples_by_season": {
      "spring": [
        "SAMN44468591",
        "SAMN44468592",
        "SAMN44468593"
      ],
      "summer": [
        "SAMN44468594",
        "SAMN44468595",
        "SAMN44468596"
      ],
      "autumn": [
        "SAMN44468597",
        "SAMN44468598",
        "SAMN44468599"
      ]
    },
    "read_processing": {
      "trim_galore_version": "0.6.11",
      "phred_threshold": 20,
      "clip_5prime_bp_per_mate": 8,
      "clip_3prime_bp_per_mate": 8,
      "minimum_read_length_bp": 36,
      "bismark_version": "0.25.1",
      "deduplication": "paired-end deduplicate_bismark",
      "extraction": "name-sorted BAM; paired-end; comprehensive; bedGraph; no_overlap"
    },
    "metric": "read-weighted CpG methylation (%)",
    "formula": "100 * sum(methylated reads) / sum(methylated + unmethylated reads)",
    "minimum_CpG_depth": 1,
    "additional_summarization_depth_filter": null,
    "season_summary": "arithmetic mean of three sample percentages",
    "season_means_pct": {
      "spring": 73.2,
      "summer": 73.18,
      "autumn": 74.88
    },
    "summarization_script": "prepare_website_data.py",
    "summarization_script_sha256": "b5bb19820fbdb3e96d7b3f856618ab3628322fccb362dd784398a1743822b70e"
  }
}