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 mr1234 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
vg0616129303 sf0616128305 6 16129303 1.06E-10 1.06E-10
vg1127876436 sf1127404822 11 27876436 1.55E-06 1.55E-06
vg0613536356 sf0613535357 6 13536356 1.62E-06 1.62E-06
vg0819969492 sf0819966779 8 19969492 1.87E-06 1.87E-06
vg0611239376 sf0611238377 6 11239376 1.90E-06 1.90E-06
vg0311072594 sf0311071312 3 11072594 2.72E-06 2.72E-06
vg0311437556 sf0311436274 3 11437556 2.96E-06 2.96E-06
vg0913099185 sf0913098184 9 13099185 3.14E-06 3.14E-06
vg1004372176 sf1004388714 10 4372176 3.49E-06 3.49E-06
vg0433017442 sf0432832328 4 33017442 4.70E-06 4.70E-06
vg1221089137 sf1221055687 12 21089137 8.65E-06 8.65E-06