GWAS Result
Target: Protein_Y19 | Encoding: additive | SNPs after QC: 1 / 7 | Samples: 95 | Significant: 0 | λGC: 0.033
Extreme deflation (λGC = 0.033).
A lambda far below 1 is usually meaningless — most often there are too
few testable SNPs after QC (1 here) to
estimate the null distribution, or tests are highly correlated.
| Metric | Value |
|---|---|
| n_snps_input | 7 |
| n_snps_after_qc | 1 |
| maf_filtered | 2 |
| missingness_filtered | 0 |
| hwe_filtered | 4 |
| hwe_not_testable | 0 |
| ld_pruned | 0 |
| SNP ▲▼ | Chromosome ▲▼ | Position ▲▼ | Beta ▲▼ | SE ▲▼ | R² ▲▼ | P-value ▲▼ | Corrected P ▲▼ |
|---|---|---|---|---|---|---|---|
| S1LG6_4228681 | -0.0988 | 0.8055 | 0.0002 | 5.00e-01 | 5.00e-01 |
Static figures
Genotype missingness
Download PNG
Method & Provenance
- Method
- GWAS — association analysis
- Method key
gwas(result type:gwas_result, result #28)- Engine
- Python · scikit-learn/statsmodels v1.8.0
- Dataset(s)
- #725 gallery — example_gwas_protein.csv
- Status
- completed
- Permanent link
- https://cat-g-omxpert.wishartlab.com/results/by-token/abdb9fb3c3284f0dbf813675034bb8b8 Bookmark or share this URL — it does not depend on your session.
- Created
- 2026-09-21 02:18:44.740736
Parameters used
| Parameter | Value |
|---|---|
target_column | Protein_Y19 |
encoding_model | additive |
significance_threshold | 0.05 |
n_snps_input | 7 |
n_snps_after_qc | 1 |
n_samples | 95 |
n_significant | 0 |
lambda_gc | 0.032914142178984904 |
Execution trace
Reconstructed from the parameters stored with this result — represents the Python/R calls the analysis service made.
# app.services.gwas_qc_service — SNP QC + allele encodingfrom sklearn.linear_model import LogisticRegressionfor snp in snp_matrix.columns: # per-SNP association test model = LogisticRegression(max_iter=1000).fit(X_snp, y) p = association_pvalue(model)fdr = statsmodels.stats.multitest.multipletests(p_values, method='fdr_bh')