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 mr1821 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
vg0229966285 sf0229960416 2 29966285 3.43E-07 3.43E-07
vg0513549188 sf0513491735 5 13549188 1.80E-06 1.80E-06
vg0111406406 sf0111405382 1 11406406 3.32E-06 3.32E-06
vg0626149778 sf0626148781 6 26149778 3.39E-06 3.39E-06
vg1222451825 sf1222418264 12 22451825 3.49E-06 3.49E-06
vg1105670701 sf1105666453 11 5670701 3.70E-06 3.70E-06
vg0141973334 sf0141972291 1 41973334 3.89E-06 3.89E-06
vg1125170215 sf1124704055 11 25170215 4.20E-06 4.20E-06
vg0508350184 sf0508350112 5 8350184 4.50E-06 4.50E-06
vg1104794411 sf1104790313 11 4794411 5.39E-06 5.39E-06