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 mr1372 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
vg1212214384 sf1212211722 12 12214384 9.56E-07 9.56E-07
vg0420556306 sf0420384350 4 20556306 1.17E-06 1.17E-06
vg0813739257 sf0813736543 8 13739257 2.46E-06 2.46E-06
vg0123570452 sf0123569408 1 23570452 2.50E-06 2.50E-06
vg0433017442 sf0432832328 4 33017442 2.53E-06 2.53E-06
vg0103370208 sf0103369208 1 3370208 4.30E-06 4.30E-06
vg1105795032 sf1105790784 11 5795032 4.57E-06 4.57E-06
vg0400842554 sf0400841554 4 842554 4.69E-06 4.69E-06