RiceVarMap v3.0

Haplotype Network Analysis:

Please input SNP IDs (the number of SNPs < 100) for this analysis (e.g., vg0122375601, vg0122375642, vg0122375884, vg0122375947, vg0122375984, vg0122376428, vg0122376434, vg0122376509, vg0122376511, vg0122376514, ). You can choose different group set to do this analysis.

Indica, Japonica and Intermediate (Indica group includes Indica I, Indical II, Indica III, Indica Intermediate and Aus. Japonica group includes Temperate Japonica, Tropical Japonica and Japonic Intermediate. Intermediate group includes Aromatic and other accessions).

Japonica, Aus and Intermediate (Indica group includes Indica I, Indica II, Indica III and Indica Intermediate. Japonica group includes Temperate Japonica, Tropical Japonica and Japonic Intermediate. Intermediate group includes Aromatic and other accessions).

Indica I, Indica II, Indica III, Indica Intermediate, Aus, Temperate Japonica, Tropical Japonica, Japonica Intermediate and Intermediate (Intermediate group includes Aromatic and other accessions)

The detailed information of the classification can be found in the "Notes and Data Evaluation" page.

Information

This module enables haplotype-based population genetic analysis by allowing users to input a set of SNP variants and explore the resulting haplotype structure across rice subpopulations. The results are presented as an integrated haplotype network and haplotype heatmap, facilitating visualization of genetic relationships and population composition.

Flexible Subpopulation Grouping: Users can select different subpopulation grouping schemes to summarize haplotype composition, enabling comparison of haplotype distributions across major rice population structures.

Haplotype Network Visualization: The haplotype network provides an intuitive representation of genetic relationships among haplotypes. Each node represents a distinct haplotype, and node size reflects haplotype frequency. Pie charts within nodes indicate the proportional contribution of different subpopulations to each haplotype.

Haplotype Heatmap: A complementary haplotype heatmap displays the genotype composition of each haplotype across all included SNP sites, allowing direct inspection of allele patterns underlying haplotype differentiation.

Filtering and Display Criteria: To ensure robustness of haplotype inference, only haplotypes supported by a minimum number of samples are displayed. Haplotypes with fewer than ten samples are excluded from visualization.