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 mr1807 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
vg0128839134 sf0128838089 1 28839134 1.86E-22 NA
vg0624160667 sf0624159670 6 24160667 8.34E-20 NA
vg1010362484 sf1010291305 10 10362484 1.37E-19 NA
vg0218470302 sf0218464433 2 18470302 1.37E-19 NA
vg0501245532 sf0501245516 5 1245532 1.54E-19 NA
vg0304677793 sf0304676795 3 4677793 1.09E-15 NA
vg0431599562 sf0431414457 4 31599562 1.05E-13 9.17E-06
vg0805653724 sf0805652727 8 5653724 NA 1.20E-07
vg0909789211 sf0909788210 9 9789211 NA 4.02E-07
vg0507128411 sf0507128353 5 7128411 NA 4.31E-06
vg0601214642 sf0601213643 6 1214642 NA 9.04E-06