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 mr1093 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
vg0216737775 sf0216731905 2 16737775 1.22E-19 1.65E-08
vg0216649351 sf0216643481 2 16649351 2.42E-19 1.08E-08
vg1216409177 sf1216406470 12 16409177 2.64E-13 NA
vg1018443385 sf1018371942 10 18443385 2.89E-13 NA
vg0519901253 sf0519838729 5 19901253 7.60E-13 NA
vg0905579820 sf0905578820 9 5579820 9.07E-13 NA