#### Data Upload Results

After successfully uploading your data, the following information becomes available throughout VIEWpoly:

##### Linkage Map Data

- **Linkage Groups**: Number of chromosomes/linkage groups detected
- **Markers**: Total number of markers in the map
- **Map Length**: Total genetic distance in centiMorgans (cM)
- **Individuals**: Number of genotyped individuals
- **Ploidy**: Detected ploidy level
- **Parental Information**: Parent names and dosages
- **Phase Information**: Linkage phase configurations

##### QTL Analysis Data

- **Phenotypes**: List of traits analyzed
- **QTL Detected**: Number of QTL identified per trait
- **QTL Positions**: Genetic and physical positions of QTL
- **LOD Scores**: Logarithm of odds scores across the genome
- **Effect Estimates**: Allelic effects for each QTL
- **Haplotype Information**: Phased haplotype data
- **Breeding Values**: Predicted breeding values for individuals

##### Genome Browser Data

- **Assembly**: Reference genome loaded and indexed
- **Annotation**: Gene models and features available (if annotated GFF/GTF provided)
- **Variants**: SNP/marker positions loaded (if VCF provided)
- **Alignments**: Read alignment tracks available (if BAM files provided)
- **Coverage**: BigWig coverage data loaded (if BigWig provided)

##### HIDECAN Data

- **GWAS Tracks**: Genome-wide association results loaded
- **Threshold**: Significance threshold applied
- **Chromosomes**: Number of chromosomes with data
- **Markers**: Total markers included in analysis
- **DE Genes**: Differentially expressed genes detected
- **Candidate Genes**: Number of candidate genes annotated

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#### Data Validation

VIEWpoly performs automatic validation checks:

 **File Format**: Verifies file extensions and structure  
 **Data Consistency**: Checks for matching marker names across files  
 **Ploidy Validation**: Ensures dosage values match specified ploidy  
 **Coordinate Systems**: Validates genetic and physical positions  

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#### Reset and Resubmit

- **Reset buttons**: Clear specific data types without affecting others
- **Reset all**: Clears all uploaded data and returns to initial state
- **Resubmit**: Upload new data to replace existing data

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#### Export Options

**Download VIEWpoly Dataset**: 

After uploading map and QTL data, you can export a consolidated dataset in VIEWpoly format for:
- Sharing with collaborators
- Future sessions
- Archival purposes
- Integration with other tools

The exported `.RData` file contains all map and QTL information but excludes large genome browser files.

### 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/)

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

**HIDECAN Documentation**: [https://plantandfoodresearch.github.io/hidecan/](https://plantandfoodresearch.github.io/hidecan/)

**GWASpoly Tutorial**: [https://potatobreeding.cals.wisc.edu/software/](https://potatobreeding.cals.wisc.edu/software/)

**Tools for Polyploids**: [https://www.polyploids.org/](https://www.polyploids.org/)

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