## VIEWgenome - Results Description

### QTL Genomic Context

**Integrated View**:
- QTL positions mapped to genome assembly
- Genetic and physical positions aligned
- Confidence intervals visualized on genome

---

### Gene Annotation Results

**Candidate Genes**:
- All genes within QTL confidence intervals listed
- Functional annotations displayed (when available)
- Gene structure visualized in browser

**Annotation Details**:
- Gene ID (systematic name)
- Gene symbol/common name
- Product description
- Genomic coordinates
- Strand orientation
- Number of exons/introns

**Functional Categories**:
- GO terms (when available)
- KEGG pathways
- InterPro domains
- Protein families

---

### Recombination Landscape

**Physical vs Genetic Distance**:
- Recombination rate variation across chromosomes
- Hotspots and coldspots identified

**Interpretation**:
- Steep slopes = high recombination
- Flat regions = suppressed recombination
- Non-monotonic patterns = structural variants

**Breeding Implications**:
- Difficult to break linkage in low-recombination regions
- High-recombination regions allow fine mapping
- Affects marker-assisted selection strategies

---

### Candidate Gene Prioritization

**Evidence Integration**:
- Genes within QTL intervals
- Expression patterns
- Functional annotations

---

### Troubleshooting

**If genes don't appear**:
- Check GFF3 file format
- Verify chromosome naming matches assembly
- Ensure proper indexing (.tbi files)

**If positions don't match**:
- Verify same genome version for all files
- Check coordinate system (0-based vs 1-based)
- Validate marker positions

**Performance issues**:
- Use hosted URLs for large files
- Reduce number of active tracks
- Zoom to specific regions
- Clear browser cache

### Additional Resources

**JBrowse Documentation**: [https://jbrowse.org/jb2/](https://jbrowse.org/jb2/)

**VIEWpoly Tutorial**: [https://cristianetaniguti.github.io/viewpoly_vignettes/](https://cristianetaniguti.github.io/viewpoly_vignettes/)

