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 mr1398 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
vg0118219645 sf0118218599 1 18219645 1.88E-13 NA
vg1013744225 sf1013672994 10 13744225 2.94E-13 NA
vg0906451223 sf0906450223 9 6451223 4.14E-13 NA
vg1121159482 sf1120693361 11 21159482 9.66E-13 NA
vg0410598528 sf0410589227 4 10598528 1.51E-12 NA
vg1009329663 sf1009258484 10 9329663 7.94E-10 NA
vg0919666357 sf0919665947 9 19666357 1.48E-09 NA
vg0205285484 sf0205285482 2 5285484 NA 2.33E-06