{
  "created_utc": "2026-09-03T18:19:23.744245+00:00",
  "method": {
    "reference_pool": "all pre-cap candidates intersected with the KING unrelated set and genotype-QC thresholds, de-duplicated against all 349 directly available raw Italian samples",
    "population_unit": "38 Europe-only or 48 Europe plus Middle East curated source-population labels; 1KG TSI is retained as a distinct fitting population rather than folded into Italy_C",
    "individual_weight": "1 divided by max(population sample count, 30)",
    "population_total_weight": "min(1, population sample count / 30) before global mean-one normalization",
    "weighted_allele_frequency": "sum(weight * allele dosage) divided by 2 * sum(observed weight)",
    "pca": "SVD of one mean centered and variance-standardized genotype vector per curated population, with each population vector multiplied by sqrt(min(1, n/30)) before global normalization",
    "within_population_variation": "used to estimate population means and individual projections, but excluded from determining the population-map axes",
    "reference_coordinates": "unweighted projection onto the fitted loadings for every included individual",
    "country_inclusion": "Italy contributes through Italy_N, Italy_C, Italy_S and a distinct 1KG TSI population, using 349 directly available raw Italian samples; four projection-only HGDP records are not substituted. France-linked samples retain French, Basques, Provence or Corsica population labels. Fine localities do not become fitting units."
  },
  "candidate_audit": {
    "precap_candidates": 2546,
    "unrelated_candidates_before_italian_deduplication": 2538,
    "unrelated_candidates": 2530,
    "deduplicated_current_italian_raw_n": 8,
    "model_specific_qc": true,
    "unique_excluded_ids": [
      "HG00124.SG",
      "NA20526.SG"
    ]
  },
  "models": [
    {
      "model": "balanced_europe",
      "reference_n": 2485,
      "population_count": 38,
      "marker_count": 8180,
      "included_italian_n": 349,
      "preexisting_reference_n": 2136,
      "population_full_weight_threshold_n": 30,
      "maximum_population_total_weight_error": 5.684341886080802e-14,
      "minimum_first_10_seed_check_loading_correlation": 0.9998915273346672
    },
    {
      "model": "balanced_europe_middle_east",
      "reference_n": 2877,
      "population_count": 48,
      "marker_count": 3111,
      "included_italian_n": 349,
      "preexisting_reference_n": 2528,
      "population_full_weight_threshold_n": 30,
      "maximum_population_total_weight_error": 5.684341886080802e-14,
      "minimum_first_10_seed_check_loading_correlation": 0.9615957642144038
    },
    {
      "model": "balanced_europe_matched_markers",
      "reference_n": 2485,
      "population_count": 38,
      "marker_count": 3111,
      "included_italian_n": 349,
      "preexisting_reference_n": 2136,
      "population_full_weight_threshold_n": 30,
      "maximum_population_total_weight_error": 5.684341886080802e-14,
      "minimum_first_10_seed_check_loading_correlation": 0.9998087765251558
    },
    {
      "model": "france_inclusive_population_weighted",
      "reference_n": 2877,
      "population_count": 48,
      "marker_count": 3111,
      "included_mapped_france_n": 329
    }
  ],
  "bootstrap_stability": [
    {
      "model": "balanced_europe",
      "PC": "PC1",
      "bootstrap_replicates": 30,
      "minimum_aligned_correlation": 0.9906593971650987,
      "median_aligned_correlation": 0.9937037383999984
    },
    {
      "model": "balanced_europe",
      "PC": "PC2",
      "bootstrap_replicates": 30,
      "minimum_aligned_correlation": 0.921917311080513,
      "median_aligned_correlation": 0.9567633602583264
    },
    {
      "model": "balanced_europe",
      "PC": "PC3",
      "bootstrap_replicates": 30,
      "minimum_aligned_correlation": 0.29416638484336755,
      "median_aligned_correlation": 0.7320657566553779
    },
    {
      "model": "balanced_europe_middle_east",
      "PC": "PC1",
      "bootstrap_replicates": 30,
      "minimum_aligned_correlation": 0.9960645469804291,
      "median_aligned_correlation": 0.9966252717147064
    },
    {
      "model": "balanced_europe_middle_east",
      "PC": "PC2",
      "bootstrap_replicates": 30,
      "minimum_aligned_correlation": 0.9612440702339342,
      "median_aligned_correlation": 0.9724475255708483
    },
    {
      "model": "balanced_europe_middle_east",
      "PC": "PC3",
      "bootstrap_replicates": 30,
      "minimum_aligned_correlation": 0.8129443950816581,
      "median_aligned_correlation": 0.9059625497687709
    }
  ]
}