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 mr1409 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
vg0216896614 sf0216890744 2 16896614 2.95E-10 2.21E-06
vg0217018976 sf0217013106 2 17018976 3.82E-09 2.11E-06
vg0216664283 sf0216658413 2 16664283 4.84E-08 8.54E-07
vg0334986236 sf0334979106 3 34986236 5.82E-07 5.23E-07
vg0524244054 sf0524181473 5 24244054 2.32E-06 3.33E-06
vg1109530326 sf1109524903 11 9530326 2.48E-06 9.55E-06
vg0820796944 sf0820794231 8 20796944 3.11E-06 1.48E-06
vg0325762988 sf0325761006 3 25762988 7.66E-06 5.68E-06