Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1890 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0334602600 sf0334595470 3 34602600 7.01E-46 NA
vg0828256208 sf0828253494 8 28256208 3.36E-45 1.52E-06
vg0206383144 sf0206383144 2 6383144 1.13E-44 4.85E-06
vg0522272712 sf0522210153 5 22272712 2.18E-44 NA
vg0823332826 sf0823330113 8 23332826 1.59E-43 NA
vg0717008460 sf0717007467 7 17008460 5.06E-43 1.59E-06
vg1016529139 sf1016457912 10 16529139 9.50E-42 9.39E-07
vg1213066313 sf1213063652 12 13066313 NA 2.07E-06
vg0711420049 sf0711419055 7 11420049 NA 2.47E-06
vg0402100710 sf0402096304 4 2100710 NA 4.66E-06