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 mr1015 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
vg0133458683 sf0133457639 1 33458683 2.42E-10 2.42E-10
vg0819433740 sf0819431027 8 19433740 1.29E-07 1.29E-07
vg0524064354 sf0524001774 5 24064354 9.01E-07 9.01E-07
vg0210314544 sf0210314542 2 10314544 9.21E-07 9.21E-07
vg0916639724 sf0916638723 9 16639724 1.41E-06 1.41E-06
vg0909373542 sf0909372541 9 9373542 1.52E-06 1.52E-06
vg0313767191 sf0313765908 3 13767191 3.30E-06 3.30E-06
vg0712960415 sf0712959422 7 12960415 3.32E-06 3.32E-06