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 mr1509 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
vg1020389432 sf1020317912 10 20389432 2.29E-56 9.77E-12
vg0332651081 sf0332643952 3 32651081 3.78E-48 NA
vg0132925911 sf0132924867 1 32925911 1.35E-47 NA
vg1014789649 sf1014718415 10 14789649 1.41E-47 NA
vg1227425580 sf1227391980 12 27425580 2.98E-47 NA
vg1001246161 sf1001245138 10 1246161 NA 2.75E-07
vg0619726119 sf0619725122 6 19726119 NA 4.69E-06
vg1001376210 sf1001375187 10 1376210 NA 5.79E-06