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 mr1360 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
vg0416930919 sf0416758961 4 16930919 3.39E-07 3.39E-07
vg0403579142 sf0403574744 4 3579142 4.10E-07 4.10E-07
vg1022609740 sf1022538214 10 22609740 7.23E-07 7.23E-07
vg0309690725 sf0309689661 3 9690725 7.92E-07 7.92E-07
vg1010749619 sf1010678440 10 10749619 8.11E-07 8.11E-07
vg1003099410 sf1003098387 10 3099410 1.59E-06 1.59E-06
vg0909184912 sf0909183911 9 9184912 1.60E-06 1.60E-06
vg1126382552 sf1125910965 11 26382552 1.61E-06 1.61E-06
vg0124089174 sf0124088130 1 24089174 2.62E-06 2.62E-06
vg0819474156 sf0819471443 8 19474156 3.69E-06 3.69E-06
vg0906910944 sf0906909944 9 6910944 3.81E-06 3.81E-06
vg0318010651 sf0318009433 3 18010651 4.47E-06 4.47E-06