RiceVarMap v3.0

Search for genomic regional variations

You can enter a genomic range to search for variations and also select a major allele frequency range to filter for variations. Detailed information on population classification can be found on the "Notes and Data Evaluation" page.

Chromosome conditions (Required)

example: chr01 : 10000 - 20000

Reference Genome:

Chromosome:

Variation Type:

Position range: < 100 kb

Population-based frequency filters

Population 1

Frequency range

Combine with

Population 2

Frequency range

Combine with

Population 3

Frequency range

Selecting which populations show the frequency of primary alleles

Note: By default, only the primary allele frequencies of the variant in the entire population are displayed. You can get the major allele frequencies for different populations by selecting the corresponding checkboxes.

Populations: All / None

All

All Indica

All Japonica

Aus

Indica I

Indica II

Indica III

Temperate Japonica

Topical Japonica

Reset

Information

This module allows users to precisely retrieve variant information within specific regions of the rice genome by chromosomal location. You can query genotype details for Single Nucleotide Polymorphisms (SNPs), Insertions/Deletions (InDels), and Short Tandem Repeats (STRs), and obtain their genotype frequency data across subpopulations such as indica, japonica, and aus.

Variant Query: Input a chromosomal region to return all variant sites within that interval, including the reference genome sequence (Reference), primary genotype (Primary), and secondary genotype (Secondary) for each site.

Frequency Filtering: Filter results by setting genotype frequency ranges for specific subpopulations (e.g., indica, japonica). Multiple conditions can be combined using "AND/OR" logic to identify variants with particular population distribution patterns.

Data Sources:

IRGSP-1.0 (Japonica Reference; Kawahara et al, 2013): Based on resequencing alignment of 4,726 accessions (4K dataset; Zhao et al, 2021), containing SNP, InDel, and STR variants.
ZS97RS3/MH63RS3 (Indica References; Song et al., 2021): Based on resequencing alignment of 3,024 accessions (3K dataset; Wang et al, 2018), providing SNP variant information.
Data Origin: Variant data originates from the International 3K Rice Genomes Project. Original data and descriptions can be accessed via the project page.