More data are still under amendment.
1.1 - Select one trait to show the phenotype data of the whole set or subset of 3K-RG.
1.2 - Upload a phenotype file for 3K-RG to display. Only ".csv" (comma splited) and ".txt" (tab splited) files are allowed.
There are three types of inputs for haplotype analysis: "Gene Locus ID", "Chromosome Region" and "SNP sites".
2.1 - Gene Locus ID
| "Gene ID" |
Gene locus from IRGSP-1.0 (e.g. Os05g0187500) or MSU7.0 (e.g. LOC_Os09g26999). |
| "Gene region" |
Choose one gene structure. When you choose the option "CDS - codon", the synonymous SNP (does not change the encoded amino acid) will be displayed as lower-case.
|
| "Filtered by MAF" |
Filter the SNP by minor allele frequency. |
| "Accessions" |
Choose the samples you used for analysis. You can use 3024 accessions by default, or paste your samples by choose "submit your population". |
| "Phenotype" |
You can choose up to 3 phenotypes provided by RFGB, or you can upload a '.csv' or '.txt' file contains phenotypic data of 3K-RG. Note: each column of '.txt' file should be splited by tab. |
2.2 - Chromosome Region
| "Region" |
A physical region on chromosome with size up to 5 kb. |
| "Filtered by MAF" |
Filter the SNP by minor allele frequency. |
| "Accessions" |
Choose the samples you used for analysis. You can use 3024 accessions by default, or paste your samples by choose "submit your population". |
| "Phenotype" |
You can choose up to 3 phenotypes provided by RFGB, or you can upload a '.csv' or '.txt' file contains phenotypic data of 3K-RG. Note: each column of '.txt' file should be splited by tab. |
2.3 - SNP Sites
| "SNPs" |
Use SNP loci as input. No more than 10 SNPs is allowed for analysis. |
| "Accessions" |
Choose the samples you used for analysis. You can use 3024 accessions by default, or paste your samples by choose "submit your population". |
| "Phenotype" |
You can choose up to 3 phenotypes provided by RFGB, or you can upload a '.csv' or '.txt' file contains phenotypic data of 3K-RG. Please note that each column of '.txt' file should be splited by tab. |
2.4 - Haplotype Result
There are four parts in the result page from haplotype analysis: "Summary of Input", "SNPs", "Haplotype Info" and "Statistics Info".
2.4.1 - Summary of input.
2.4.2 - SNPs. You can download the SNPs used for haplotype analysis in this part.
2.4.3 - Haplotype Info. You can download the result file of haplotype analysis in this part.
Violin plot (generated by ggplot2) indicates the effect of haplotypes on one trait. If you are stucked at the plotting page (more than 2 minutes), please set your browser allowing the POP-UPS of RFGB.
2.4.4 - Statistics Info. Results of "equality of variances", "ANOVA" and "t-tests" are displayed in this part.
To compare the phenotypic differences between haplotypes, a methodology based on one-way ANOVA-protected Tukey’s multiple pair-wised comparison was carried out based on the following two steps.
a) One-way AVNOA based on following formula:
F=(MS(Haps))/MSE, where MS(Haps) refers to the mean square value calculated based on the phenotypic value of all haplotypes, and MSE stands for the mean square value of errors.
b) Tukey’s t-test based on following formula:
t=((x̅1) - (x̅2)/(S/√(n-1)), where (x̅1) and (x̅2) refer to the mean values of phenotypic effects of one pair of haplotypes, while S refers to the standard deviation of all the pairs, and n refers to the sample size.
Note that for some minor alleles/haplotypes, "Diff." should be regarded as important as "p-value" in the "t-test" results.
3.1 - Main framework of RFGB.
3.2 - Development tools used in RFGB.
RFGB (Rice Function Genomics and Breeding Database) is constructed based on LAMP (Linux, Apache, MySQL and PHP).
Functional analysis is performed by Perl and R, and part of visualization is based on JavaScript. JBrowse is used to display genome variations.
