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 mr1844 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
vg1215178307 sf1215175643 12 15178307 3.30E-09 2.84E-06
vg1214822308 sf1214819649 12 14822308 1.78E-08 2.73E-06
vg0721298960 sf0721297967 7 21298960 2.30E-08 NA
vg0229918162 sf0229912293 2 29918162 6.32E-08 9.51E-06
vg1104990849 sf1104986660 11 4990849 6.59E-08 6.35E-06
vg0723991123 sf0723990129 7 23991123 2.04E-06 NA
vg0324083783 sf0324081862 3 24083783 3.97E-06 6.71E-06
vg0300249514 sf0300248514 3 249514 NA 3.43E-06