### QTL Profile Results

**Significance Score Display**:
- Significance scores (LOD or -log10(p-value)) plotted across linkage group
- Continuous curve showing QTL evidence along chromosome
- Peaks indicate potential QTL positions
- Adjust map range to highlight corresponding region on genetic map

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### Genetic Map Results

**Map Display**:
- Horizontal representation of linkage groups
- Marker positions shown as vertical lines along chromosome
- Genetic distances displayed in centiMorgans (cM)
- Markers color-coded by SNP base (A, T, C, G)

**Single Linkage Group View**:
- Detailed view of one chromosome region according to selected map range
- All markers visible with positions

**Multiple Linkage Group View**:
- Side-by-side comparison of all linkage groups
- Compare map lengths across chromosomes
- Overall genome architecture visible
- Identify marker distribution patterns

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### Map Summary Statistics Results

**Global Statistics Displayed**:
- **Total map length** per linkage group (cM)
- **Total number of markers** across entire map
- **Average marker spacing** (mean distance in cM)
- **Largest gap** between consecutive markers
- **Marker type distribution**: 
  - Simplex markers count
  - Double-simplex markers count
  - Multiplex markers count

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### Parental Haplotypes Results

**Haplotype Displayed in Graphic**:
- Parent 1 and 2 haplotypes shown as colored segments
- Each row represents a parental haplotype
- Markers ordered by genetic position along chromosome

**Haplotype Table**:
- Phased parental haplotypes shown as SNP base table
- Each parent's haplotypes organized in columns
- Markers ordered by genetic position (rows)
- SNP bases (A, T, C, G) displayed for each homolog

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### Download Results

**Available Exports**:

**Map Images**:
- High-resolution plots of genetic maps
- Formats: PNG, TIFF, JPEG, PDF
- Customizable dimensions for publications
- Includes QTL overlays if phenotype selected

**Data Tables**:
- **Map summary statistics**: CSV, Excel, or PDF format
  - Linkage group information
  - Marker counts and spacing
  - Map lengths and gaps
- **Parental haplotypes**: CSV, Excel, or PDF format
  - SNP bases for each parent
  - Marker positions
  - Haplotype phase information

**Export Uses**:
- Publication-ready figures
- Supplementary data tables
- Further analysis in other software
- Archive for reproducibility

### Additional Resources

**MAPpoly Tutorial**: [https://mmollina.github.io/MAPpoly/](https://mmollina.github.io/MAPpoly/)

**polymapR Manual**: [https://cran.r-project.org/web/packages/polymapR/](https://cran.r-project.org/web/packages/polymapR/)

**OneMap Documentation**: [https://cran.r-project.org/web/packages/OneMap/](https://cran.r-project.org/web/packages/OneMap/)

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

**Breeding Insight**: [https://www.breedinginsight.org](https://www.breedinginsight.org)
