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 mr1509 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
vg1219062101 sf1219033537 12 19062101 6.86E-08 NA
vg1207573581 sf1207570986 12 7573581 1.07E-07 4.05E-06
vg0225367493 sf0225361624 2 25367493 1.30E-07 2.97E-06
vg0235108715 sf0235102846 2 35108715 4.52E-07 NA
vg1208658349 sf1208655756 12 8658349 5.42E-07 7.38E-06
vg1001246161 sf1001245138 10 1246161 7.00E-07 1.88E-06