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 mr1762 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
vg0141203398 sf0141202355 1 41203398 2.18E-10 NA
vg0422580400 sf0422395283 4 22580400 3.78E-10 NA
vg0101328049 sf0101327049 1 1328049 4.41E-10 NA
vg0315387307 sf0315385954 3 15387307 5.31E-10 NA
vg0205949916 sf0205949916 2 5949916 6.30E-10 NA
vg0630863292 sf0630862294 6 30863292 2.04E-08 8.92E-06
vg0427140714 sf0426955584 4 27140714 3.36E-06 1.14E-06
vg0518984986 sf0518922470 5 18984986 NA 6.59E-07
vg0528097164 sf0528034519 5 28097164 NA 1.81E-06
vg0525001887 sf0524939302 5 25001887 NA 2.98E-06
vg1219736727 sf1219708197 12 19736727 NA 5.49E-06