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 mr1520 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
vg1106471446 sf1106467198 11 6471446 5.25E-07 5.26E-07
vg0905969651 sf0905968651 9 5969651 3.81E-06 3.81E-06
vg0129989388 sf0129988343 1 29989388 3.85E-06 3.85E-06
vg0123284887 sf0123283843 1 23284887 3.85E-06 3.86E-06
vg1203723153 sf1203722152 12 3723153 4.40E-06 4.40E-06