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 mr1156 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
vg0414235746 sf0414226459 4 14235746 1.69E-11 1.31E-07
vg0408179042 sf0408174316 4 8179042 9.50E-11 4.88E-07
vg1013655531 sf1013584300 10 13655531 2.31E-10 NA
vg1010568067 sf1010496888 10 10568067 2.58E-10 NA
vg0310837058 sf0310835776 3 10837058 2.96E-10 NA
vg0712000398 sf0711999404 7 12000398 9.52E-09 NA
vg0223948926 sf0223943057 2 23948926 1.57E-08 1.92E-06
vg0222749778 sf0222743909 2 22749778 2.12E-08 NA
vg1213231314 sf1213228652 12 13231314 7.46E-08 NA
vg1216719017 sf1216712971 12 16719017 NA 2.87E-07