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 mr1785 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
vg0319023309 sf0319022069 3 19023309 1.86E-10 7.92E-06
vg0320096298 sf0320094809 3 20096298 1.47E-09 NA
vg0407141000 sf0407136270 4 7141000 1.69E-09 NA
vg0218153756 sf0218147887 2 18153756 2.70E-09 2.78E-06
vg0402237327 sf0402232922 4 2237327 3.28E-09 NA
vg0432694182 sf0432509071 4 32694182 4.26E-09 3.10E-06
vg0402405140 sf0402400735 4 2405140 6.57E-09 5.29E-06
vg0432486247 sf0432301139 4 32486247 3.16E-08 7.56E-07
vg0433253554 sf0433068442 4 33253554 NA 3.36E-06
vg0220021692 sf0220015824 2 20021692 NA 3.92E-06