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 mr1687 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
vg0406853125 sf0406848570 4 6853125 2.83E-08 2.83E-08
vg0406888519 sf0406883778 4 6888519 5.01E-07 5.01E-07
vg0412011347 sf0412002058 4 12011347 1.08E-06 1.08E-06
vg0406400649 sf0406396089 4 6400649 1.16E-06 1.16E-06
vg1001446636 sf1001445613 10 1446636 2.02E-06 2.02E-06
vg0402100710 sf0402096304 4 2100710 4.78E-06 4.78E-06
vg0527138830 sf0527076186 5 27138830 4.81E-06 4.81E-06