For 2-variety comparison: display only allele mismatches
between the two queried varieties.
For all varieties: display only varieties with at
least one mismatch with the reference.

Use only the top N distances between variety pairs to construct the phylogenetic tree. Only varieties in these pairs are included in the tree.

Minimum number of mismatches to branch in the tree.
Below this number, the varieties are grouped
into one node.

Color the SNPs based on mismatch with the reference.

Search only on varieties in your selected list.
The list can be created from My Lists in the menu or from the result of Search > Varieties .

Get only alleles from positions in the list.
The list can be created in My List in the menu.

Get only alleles within the loci in the list.
The list can be created from My Lists in the menu or from the result of Search > Gene loci.

Color the SNPs based on allele value.

Use only the core SNPs

Recount mismatch in queried region only.

Add another allele filter.

Include synonymous SNPs.

Color synonymous SNPs in gray.

Exclude non-synonymous SNPs and varieties with no non-synonymous SNPs in the queried regions.

Query SNPs.

Highlight splice variant SNPs.

Show indels as sequence alignments.

Include indels. Disabled for SNP and locus lists

Download Plink format. Disabled for Indels.

Download Flapjack format. Disabled for Indels.

Show all SNPs.

Show non-synonymous SNPs only.

Show non-synonymous and splice site SNPs.

Show all SNPs, highlight the non-synonymous.

Include SNPs in splice donor and acceptor sites in non-synonymous.

Displays the variant table.

If checked, will consider heterozygous indels. Otherwise will use only allele1 only.

Downloads the Fasta file of alternate sequence without displaying the table.

Show alleles from the other 4 reference genomes which aligned with the queried reference region. Will disable indels.

Match the genotype (SNP list with alleles) to all varieties in the dataset.

Match the selected variety with the other varieties in the dataset.

How missing alleles in the varieties are counted in genotype comparison.

Snp set to query. (All-32M multiallelic, the default in previous SNP-seek version; Base-18M biallelic and heterozygosity within HW expectation; Filtered-4.8M alt allele frquency at least 0.01; Core-404k LD pruned). Detailed desription in Download section.

We currently disable the reference genome selection because we realized that we are inadvertently imposing a pan-genome for rice. The SNPs in other reference genomes were determined using the best aligned regions from the pair-wise comparison between the five reference genome, and we progressively identified genome regions unique to each of each reference genomes in an arbitrary manner (Nipponbare -> 9311 -> ir64 -> dj123 -> kasalath), which may result in ambiguous SNP locations between reference genomes. Although we selected the best alignment (by length and % identity), these are local and not guaranteed correct because aligned regions are not unique nor symmetric, and other considerations (biological or computational), or global optimization may be necessary to assign the best genome-wide alignments. To improve this, we are currently working to display the matrix of samples X SNPs/indels as identified for each reference genome, which we will soon publish in SNP-Seek. Our next big project would to be to do the comparative genomics for all the currently published high quality rice genomes,which allows you to unambiguously map SNPs in each genome.

If this data is necessary and urgently needed for your work now, we recommend you use the VCF files of the SNPs/indels identified for the other reference genomes at our S3 site (pls see iric.irri.org/resources/3000-genomes-project for details) and use external tools to extract regions of the VCF files. In the Rice Galaxy resource at galaxy.irri.org, this can be done using --> , one VCF at a time.