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 mr1812 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
vg0805946030 sf0805945033 8 5946030 1.02E-08 2.93E-06
vg0321576069 sf0321574579 3 21576069 1.81E-08 6.79E-07
vg0124420479 sf0124419435 1 24420479 5.36E-08 NA
vg1001247868 sf1001246845 10 1247868 7.93E-08 1.44E-06
vg0222002131 sf0221996262 2 22002131 1.87E-07 4.40E-06
vg0724377253 sf0724376259 7 24377253 2.92E-07 3.46E-06