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 mr1732 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
vg0140642543 sf0140641500 1 40642543 1.48E-11 NA
vg0619791673 sf0619790676 6 19791673 5.40E-11 NA
vg1122863147 sf1122397018 11 22863147 7.23E-11 4.28E-06
vg0429773519 sf0429588388 4 29773519 8.57E-11 NA
vg0614652165 sf0614651166 6 14652165 1.05E-10 NA
vg1218416620 sf1218388056 12 18416620 1.07E-10 4.64E-06
vg0429835631 sf0429650501 4 29835631 1.17E-10 NA
vg0619806827 sf0619805830 6 19806827 1.08E-09 NA
vg1208270520 sf1208267925 12 8270520 5.18E-09 1.06E-06
vg0918838703 sf0918837703 9 18838703 5.07E-08 2.63E-06
vg0516242828 sf0516185310 5 16242828 1.34E-07 4.57E-06
vg0528557932 sf0528495287 5 28557932 2.98E-06 NA
vg0134429681 sf0134428638 1 34429681 NA 2.49E-06