For 2-variety comparison: display only allele
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
Below this number, the varieties are
into one node.
Color the SNPs based on mismatch with the
Search only on varieties in your selected
The list can be created from My Lists
in the menu or from the result of Search >
Get only alleles from positions in the
The list can be created in My List in
Get only alleles within the loci in the
The list can be created from My Lists
in the menu or from the result of Search > Gene
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.
Highlight splice variant SNPs.
Show indels as sequence alignments.
Include indels. Disabled for SNP and locus
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.
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.