In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

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/

VIEWpoly Tutorial: https://cristianetaniguti.github.io/viewpoly_vignettes/

viewpoly documentation built on July 11, 2026, 1:08 a.m.