{
  "initial_F1": 126,
  "final_F1": 126,
  "SNPs": 1109918,
  "LD_pruned_SNPs": 434572,
  "per_chr_QC_counts": {
    "1": 188379,
    "2": 159241,
    "3": 164713,
    "4": 127504,
    "5": 109120,
    "6": 128372,
    "7": 131783,
    "8": 102199
  },
  "dosage_variability_QC": {
    "markers_before": 1111311,
    "nonsegregating_dosage_removed": 1393,
    "markers_after": 1109918,
    "criterion": "at least2 observed diploid genotype classes; constant heterozygosity excluded; no phenotype based selection"
  },
  "excluded_after_sample_QC": [],
  "duplicate_genotype_patterns": [],
  "phenotype_diagnostics": {
    "n": 126,
    "minimum_percent": 0.297,
    "maximum_percent": 15.1398238196888,
    "mean_percent": 4.7439319592342875,
    "median_percent": 4.680761241701489,
    "SD_percent": 2.239902412114146,
    "PC_adjusted_residual_Shapiro_W": 0.9606744647026062,
    "PC_adjusted_residual_Shapiro_p": 0.0010274583473801613,
    "max_abs_standardized_residual": 4.38731827303967,
    "flagged_abs_standardized_gt3": [
      "F1-78"
    ],
    "policy": "descriptive diagnostic only; no samples removed or phenotype transformed based on this test"
  },
  "specification": {
    "biallelic_SNPs_only": true,
    "chromosomes": [
      1,
      2,
      3,
      4,
      5,
      6,
      7,
      8
    ],
    "minimum_sample_genotype_DP": 5,
    "maximum_variant_missingness": 0.1,
    "minimum_MAF": 0.05,
    "maximum_sample_missingness": 0.15,
    "HWE_filter": "not applied to F1 family",
    "LD_pruning": {
      "window_kb": 50,
      "step_variants": 5,
      "r2": 0.2
    },
    "minimum_observed_genotype_classes": 2,
    "reason": "F1 fixed heterozygosity may have MAF0.5 but no dosage variability; exclude unidentifiable effects before association fitting"
  }
}