Tutorial of RiceVarMap
1. Brief introduction to RiceVarMap and its basic query function
2. Search for SNPs by a region and filter SNPs by major allele frequencies
3. Search for SNPs within a gene
4. Search for genotype using SNP IDs in multiple cultivars
5. Search for polymorphic positions between two cultivars
6. Search for INDELs (insertions or deletions) within a region
7. Search for INDELs within a gene
8. Search for genotype using INDEL IDs in multiple cultivars
9. Get the detailed information for a SNP or INDEL
10. Query SNPs or/and INDELs in a graphical genome browsing interface
11. Search for cultivar information
12. Design primer by SNP/INDEL ID
14. Haplotype network analysis
1. Brief introduction to RiceVarMap and its basic query function top
RiceVarMap is a database that contains 6,551,358 Single Nucleotide Polymorphisms (SNPs) and 1,214,627 insertions or deletions (INDELs) of 1,479 rice cultivars all over the world.
Users can search SNPs/INDELs by identifiers of the SNPs/INDELs or genomic regions, and then SNPs can be filtered by allele frequencies. Users can also identify the genomic variations of significant effects that may alter the protein sequence of a gene by searching the SNPs/INDELs using the gene identifier. Moreover, the query results are available for users to download through our website.
You can visit RiceVarMap by entering its address http://ricevarmap.ncpgr.cn.
Background of data collection, processing and evaluation could be found in Notes and Data Evaluation page.
2. Search for SNPs by a region and filter SNPs by major allele frequencies top
Select "SNP Information" and clicking "Search for SNPs by Region".
You can specify a chromosome and input a range. The result shows chromosome information, SNP ID (ID of the SNP in our database), position of the SNP, the reference genotype, the major allele in cultivars, the minor allele in cultivars and the frequency of major allele.
And you can also filter SNPs by major allele frequencies.
3. Search for SNPs within a gene top
You can select "SNP Information" and clicking "Search for SNPs within Gene" in the toolbar.
There are two tables in the webpage. You can enter one MSU Osal Rice Loci (e.g. LOC_Os01g01070), and if you want to search for SNPs in the upstream or downstream region, you can enter the upstream or downstream distance between the gene (e.g. upstream: 0.5kb, downstream 0.2kb).
The result shows SNP ID, chromosome, position, major allele, minor allele, frequency of major allele, the variation in this position and the effect or the location of this SNP.
The haplotype network plot will plot when SNP number > 3 and < 50.
SNPs will be highlighted when they have great influence on gene functions.
Users also can use the key words of gene function or gene symbol (like Cellulose synthase or ehd1) to search gene and SNPs in these gene.
4. Search for genotype using SNP IDs in multiple cultivars top
Firstly, you should collect SNP IDs you need (you can find that in "search for SNPs by region" page), and select "SNP Information" and click "Find Genotype with SNP ID". Select cultivar name and click "ADD" or click "ALL ADD", enter SNP ID (e.g. sf0100014574, sf0100014605, sf0100014986, sf0100015017, sf0100015030) and then click submit to get results.
The result shows SNP ID, chromosome, position, reference genotype, major allele, minor allele, and the genotype of the cultivar which selected. When the genotype of cultivar is consistent with the minor allele, it will be displayed in red.
5. Search for polymorphic positions between two cultivars top
You can select "SNP Information" and then click "Search for Polymorphic Positions between Two Cultivars".
Cultivar name and chromosome should be entered (e.g. Cultivar 1: C001(Sadu-cho), Cultivar 2: C006(Shan-Huang Zhan-2), Chromosome: 1) and you must enter the start position and end position.
Through the result, two aspects of information will be found. The first is information of cultivars, which include cultivar name, ID name (our sequencing number,cultivar ID), location of cultivar, the longitude and the latitude. The second is information of SNPs, which include SNP ID, chromosome, position, major allele, minor allele, reference genotype, the genotype of cultivar1 and the genotype of cultivar2.
6. Search for INDELs (insertions or deletions) within a region top
You can use "Search for INDELs by Region" page to get this information. Select "INDEL Information" and click "Search for INDELs by Region".
Enter the region you want to search, and select a chromosome. The result shows Chromosome, INDEL ID (the ID we named in our database), start position of the sequence, end position of the sequence, reference sequence, alternative sequence, the number of reference sequence, the number of alternative sequence of all cultivars.
7. Search for INDELs within a gene top
Select "INDEL Information" and click "Search for INDELs within a Gene". As "Search for SNPs within in gene", you should enter MSU Loci or with upstream and downstream information and submit.
The result shows INDEL ID, chromosome, start position, end position, reference sequence, alternative sequence, and the varition effect of the INDEL.
8. Search for genotype using INDEL IDs in multiple cultivars top
Select "INDEL Information" and click "Search for Genotype with INDEL ID".
The result shows chromosome, start position, end position, reference sequence, alternative sequence and the genotype of the cultivar.
9. Get the detailed information for a SNP or INDEL top
Select "SNP Information", click "Search for SNP information with SNP ID" and enter one SNP ID to get SNP detail information.
The result includes basic information of the SNP, allele frequencies of rice sub-populations and variation effect of the SNP.
Select "INDEL Information" and click "Search for INDEL information with INDEL ID" for detailed information of one INDEL.
The result includes basic information from this INDEL and the effect of the variation of this position.
10. Query SNPs or/and INDELs in a graphical genome browsing interface top
We achieve this by using generic genome browser (GBrowse). You should click "GBrowse" and then enter a region; select a data source and clicking "Select Tracks" to select features what you want.
The result is shown in a graphic interface, you can click the icon for more details.
11. Search for cutivar information top
The geographical information of 1,479 rice accessions is provided, and each cultivar is named with a cultivar ID (e.g. C001, HP84 and W001). The classification information and phenotype images of these rice accessions is available from this page. and we use Google map to help users to locate the position of each accession.
phenotype images of one cultivar:
12. Design primer by SNP/INDEL ID top
This tool is intended for researchers to pick PCR-primers to validate SNPs/INDELs or develop molecular markers. Primers will be designed to flank the target SNP/INDEL and avoid to overlap with known SNPs/INDELs.
In result the primer positipn, SNP and the INDEL position is marked out.
13. Design primer by region top
This tool is intended for researchers to pick PCR-primers to amplify genomic regions avoiding to overlap with known SNPs/INDELs.
14. Haplotype network analysis top
Haplotype network is frequently used in population genetic analysis, and users can download csv format and pdf file for further analysis.
