### QTL Profile Results

The QTL profile plot displays:

**Significance Score Curve**:
- Continuous line showing QTL evidence across each linkage group
- Peaks indicate potential QTL positions
- Higher scores values suggest stronger QTL
- The significance score is typically a LOD score or -log10(p-value) depending on the QTL analysis software used

**Significance Threshold**:
- Significant LOD score are indicated by the triangle on the bottom of the plot
- Threshold is pre-determined by the QTL analysis software used
- Horizontal lines around the triangle show the confidence interval for the QTL peak

**QTL Markers**:
- Triangle symbols at detected QTL positions
- Click to select for detailed analysis
- Multiple QTL/triangles can be selected simultaneously

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### QTL Effects Results

**Allelic Effects**:
- Each bar represents the estimated effect of one parental haplotype on the trait
- Values indicate the expected change in phenotype
- Positive values increase the trait
- Negative values decrease the trait

**Comparison Across QTL**:
- Effects standardized when viewing multiple QTL (circle)
- Digenic effects can be visualized via `Alleles combination` 

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### Haplotype Analysis Results

**Haplotype Blocks**:
- Colored segments represent different parental haplotypes
- Each graphic represents a progeny individual
- Each row corresponds to a parental haplotype herited by the individual
- Selected QTL position is marked with a dashed vertical line
- Only individuals contained the selected haplotypes are displayed
- Recombination events can be visualized by the change in haplotype color along the chromosome

**QTL-Associated Haplotypes**:
- Haplotypes carrying favorable alleles should be selected
- Useful for marker-assisted selection

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### Breeding Values Results

**Individual Rankings**:
- Individuals ranked by predicted breeding value
- Higher values indicate better genetic potential
- Values for each trait selected are represented in different columns
- Useful for parent selection

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### QTL Summary Results

**Detected QTL**:
- Complete list of selected significant QTL
- Multiple QTL per linkage group possible
- Organized by phenotype and chromosome

**Position Information**:
- Genetic position in centiMorgans (cM)
- Confidence interval bounds

**QTL Statistics**:
- p-values
- heritability estimates

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### Downloadable Results

All visualizations and tables can be exported:

**Plots**:
- High-resolution images for publications
- Multiple format options (PNG, TIFF, PDF)
- Customizable dimensions and resolution

**Tables**:
- Breeding values for all individuals
- Complete QTL summary statistics
- CSV/TSV formats for further analysis

**R Data Objects**:
- Save plot objects for customization
- Reload in R for additional analysis
- Preserve all plot metadata


### Additional Resources

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

**MAPpoly Tutorial**: [https://rpubs.com/mmollin/tetra_mappoly_vignette](https://rpubs.com/mmollin/tetra_mappoly_vignette)

**QTLpoly Tutorial**: [https://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial](https://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial)

**polyQTLR Tutorial**: [https://cran.r-project.org/web/packages/polyqtlR/vignettes/polyqtlR_vignette.html](https://cran.r-project.org/web/packages/polyqtlR/vignettes/polyqtlR_vignette.html)

**polymapR Tutorial**: [https://cran.r-project.org/web/packages/polymapR/vignettes/Vignette_polymapR.html](https://cran.r-project.org/web/packages/polymapR/vignettes/Vignette_polymapR.html)

**diaQTL Tutorial**: [https://jendelman.github.io/diaQTL/diaQTL_Vignette.html](https://jendelman.github.io/diaQTL/diaQTL_Vignette.html)

**OneMap Tutorial**: [https://cristianetaniguti.github.io/Tutorials/onemap/](https://cristianetaniguti.github.io/Tutorials/onemap/)
