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𧬠Linkage Map Creator v6.0
π Upload
βοΈ Parameters
π QC Report
π Results
πΊοΈ Map Plot
π Density & RF
𧬠Cytogenetic
β Help
π Upload Genotype Data
Choose Excel File (.xlsx)
Browseβ¦
Population Type:
F2
RIL
β¨ v6.0 Features:
β’ High-resolution ggplot linkage map
β’ Recombination fraction heatmap
β’ Marker density distribution plot
β’ Cytogenetic ideogram with hover tooltips
β’ Allele frequency banding per chromosome
β’ Full Excel export with all analysis sheets
π Upload Status
π¬ Data Preview (first 10 rows, converted)
𧬠Chromosome Assignments
βοΈ Analysis Parameters
Missing Data Threshold:
Max Recombination Fraction (r):
π§ͺ Chi-Square Filter
Enable chi-square segregation distortion filter
Significance level (Ξ±):
Apply Bonferroni correction
β οΈ Chi-square filtering removes markers with skewed allele ratios.
βΉοΈ Chi-square filter is OFF.
π Map Scaling
Max Total Map Length (cM):
Scaling Method:
Proportional
Uniform
βΆ Run Analysis
π Parameter Guide
Missing Data Threshold:
Markers with > this fraction missing are excluded.
Max Recombination Fraction:
Pairs with r β₯ threshold get a 50 cM gap.
Monomorphic Removal:
Automatic β fixed allele markers excluded.
Chi-Square Filter:
Optional β removes segregation-distorted markers.
Map Scaling:
Proportional scales all chromosomes uniformly; Uniform equalises chromosome lengths.
π Scaling Summary
Before Scaling
After Scaling
π Quality Control Report
ποΈ Removed Markers β Full Detail
β¬ Download Removal Log (.xlsx)
π Analysis Results
β¬ Full Excel Results
β¬ All Markers + Positions
β¬ Retained Markers List
β Retained Markers
π All Markers β Status + Positions
πΊοΈ Linkage Map Table
π Summary Statistics
Upload data and click 'Run Analysis' to see results.
π¨ Plot Options
Chromosomes:
Plot Theme:
Dark
Blue/White
Minimal White
Color Palette:
Set1
Set2
Set3
Paired
Dark2
Accent
Spectral
RdYlBu
PRGn
Show Marker Labels
Label Size:
Chromosome Width:
Marker Point Size:
LG Spacing:
Plot Height (px):
β¬ Download PNG (300 dpi)
πΊοΈ Genetic Linkage Map
Run analysis first.
π Marker Density per Chromosome
Chromosomes:
Bin Width (cM):
β¬ Download
Run analysis first.
π‘οΈ Adjacent Marker Recombination Heatmap
Chromosomes:
Max Pairs to Show:
β¬ Download
Run analysis first.
𧬠High-Resolution Cytogenetic Ideogram
Select Chromosomes:
π· Save as PNG
Zoom:
1.0Γ
Parent A (aa)
Parent B (bb)
Heterozygous (ab)
Missing / unknown
Chromosome Width:
Spacing:
px per cM:
Font Size:
Color Scheme:
Dark Ideogram
Genomics Blue
Forest
Red/Blue
Pastel
Show cM scale bar
Show marker names (β€200 markers)
Run analysis first.
π Application Guide β v6.0
Required Input Format
Excel (.xlsx): Column 1 = 'Marker', Column 2 = 'Chromosome'
Genotype columns 3+: individual sample genotype calls
Accepted codes: a / b / ab / β OR numeric 2 / 1 / 0 / β1
Chromosome column: integer numbers or Excel VLOOKUP formulas
Genotype Encoding Reference
Analysis Workflow
Upload your .xlsx genotype file in the Upload tab.
Choose population type (F2 or RIL).
Adjust QC parameters in the Parameters tab.
Click 'Run Analysis'.
View QC report, download results, and explore all visualisations.
Plots Available
Map Plot:
High-resolution ggplot linkage map with chromosome ideograms.
Density & RF:
Marker density histograms + recombination fraction heatmap.
Cytogenetic:
HTML canvas ideogram with allele-colour banding and hover tooltips.