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 mr1615 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
vg0805967435 sf0805966438 8 5967435 9.91E-07 9.93E-07
vg0819538105 sf0819535392 8 19538105 1.14E-06 1.15E-06
vg0804007001 sf0804006004 8 4007001 1.39E-06 1.40E-06
vg1210400634 sf1210398047 12 10400634 1.41E-06 1.41E-06
vg0132005092 sf0132004048 1 32005092 2.94E-06 2.94E-06