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 mr1688 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
vg0423536187 sf0423351044 4 23536187 1.46E-06 1.46E-06
vg0911637912 sf0911636911 9 11637912 1.93E-06 1.93E-06
vg0211829965 sf0211829961 2 11829965 2.78E-06 2.78E-06
vg1204319901 sf1204318889 12 4319901 4.00E-06 4.00E-06
vg1213006164 sf1213003503 12 13006164 4.78E-06 4.78E-06
vg0702444355 sf0702443356 7 2444355 4.95E-06 4.95E-06