## VIEWgenome - Parameters Description

### Select Phenotypes

**Phenotype Selection**:
- Choose one or multiple traits to visualize
- Must have QTL analysis loaded
- Filters QTL and genomic regions to display

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### Select Linkage Groups

**Linkage Group Selection**:
- Choose specific chromosomes to explore
- Correlates with QTL positions
- Zoom in genome browser view to selected regions

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### QTL Profile by Linkage Group

Displays the QTL scan profile for the selected chromosome:

**Parameters**:
- Same as VIEWqtl profile plot
- Synchronized with genome browser position
- Interactive selection of QTL peaks

**Features**:
- Move Map Range to update browser position
- Zoom into regions of interest
- Significance score threshold overlay

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### Linkage Map Position by Physical Position

**Comparative Plot**:
- Y-axis: Physical position (base pairs)
- X-axis: Genetic position (centiMorgans)
- Points: Markers

**Purpose**:
- Identify recombination rate variation
- Detect chromosomal rearrangements
- Compare genetic vs physical distances

**Interpretation**:
- Linear relationship = uniform recombination
- Non-linear regions = recombination hotspots/coldspots
- Inversions appear as reverse slopes

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### JBrowse Genome Browser

Interactive genome browser powered by JBrowseR:

**Navigation Controls**:
- **Search box**: Jump to specific coordinates or gene names
- **Zoom slider**: Adjust resolution
- **Pan**: Drag to move along chromosome
- **Chromosome selector**: Switch between chromosomes

**Track Configuration**:
- Toggle tracks on/off
- Adjust track height
- Change display modes
- Modify color schemes

**View Options**:
- Linear genome view (default)
- Multiple region comparison
- Split view for synteny

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### Genome Browser Tracks

#### Reference Sequence Track

**FASTA Assembly**:
- Displays nucleotide sequence at high zoom
- Shows GC content at low zoom
- Required for all other tracks

**Configuration**:
- Upload local `.fasta.gz` with index files
- Or provide hosted URL for faster loading

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#### Gene Annotation Track

**GFF3 Features**:
- Gene models with exon/intron structure
- CDS (coding sequences)
- UTRs (untranslated regions)
- Other genomic features

**Interactions**:
- Click features for detailed information
- Hover for quick summary
- Export feature sequences

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#### Variant Track

**VCF Data**:
- SNP and marker positions
- Allele frequencies (when available)
- Genotype information
- Overlaps with map markers

**Filters**:
- Filter by allele frequency
- Filter by quality score
- Show only map markers

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#### Alignment Track

**BAM/CRAM Files**:
- Read coverage visualization
- Individual read alignments
- Alignment quality metrics

**Display Modes**:
- Coverage histogram
- Individual reads
- Paired-end arc view

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#### Coverage Track

**BigWig Data**:
- Continuous coverage values
- Signal intensity plots
- Custom value ranges

**Applications**:
- RNA-seq coverage
- ChIP-seq signals
- Other continuous data

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### QTL Region Annotation Table

**Table Contents**:
- Genes within QTL confidence intervals
- Gene ID and name
- Start and end positions
- Strand orientation
- Functional annotations (when available)

**Features**:
- Sortable columns
- Search by gene name or ID
- Filter by position ranges
- Export to CSV/TSV

**Usage**:
- Identify candidate genes
- Explore functional annotations
- Export gene lists for enrichment analysis

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### Download Options

**Images**:
- Genome browser screenshots
- Profile plots
- Position comparison plots
- Formats: PNG, TIFF, JPEG, PDF

**Data**:
- Annotation table exports
- Gene lists in CSV/TSV
- Coordinate files

**Browser Sessions**:
- Save JBrowse configuration
- Share with collaborators
- Reload custom views

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### Navigation

- **Go to QTL**: Return to QTL analysis view
- **Go to Map**: Navigate to map visualization
- **Info button**: Access this help documentation

### 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/)
