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 mr1663 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
vg0601223619 sf0601222620 6 1223619 3.29E-08 3.29E-08
vg1125651425 sf1125185264 11 25651425 4.88E-07 4.88E-07
vg0608711440 sf0608710441 6 8711440 6.23E-07 6.23E-07
vg0913073379 sf0913072378 9 13073379 1.00E-06 1.00E-06
vg0610634320 sf0610633321 6 10634320 1.69E-06 1.69E-06
vg0329036475 sf0329029527 3 29036475 3.76E-06 3.77E-06
vg0723278269 sf0723277276 7 23278269 4.34E-06 4.34E-06