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 mr1761 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
vg0430967841 sf0430782721 4 30967841 2.10E-18 3.36E-07
vg0430942143 sf0430757023 4 30942143 2.66E-18 2.55E-08
vg0104592595 sf0104591595 1 4592595 2.35E-16 NA
vg1003192650 sf1003191627 10 3192650 7.74E-16 NA
vg0127819685 sf0127818641 1 27819685 4.47E-15 NA
vg0608148280 sf0608147281 6 8148280 4.90E-15 NA
vg0719897669 sf0719896676 7 19897669 1.20E-13 1.13E-06
vg0111431821 sf0111430797 1 11431821 2.68E-13 2.42E-06
vg0316491917 sf0316490562 3 16491917 3.85E-13 6.95E-06
vg1011166653 sf1011095473 10 11166653 6.50E-10 NA
vg0525195530 sf0525132951 5 25195530 NA 3.69E-06
vg0617302802 sf0617301805 6 17302802 NA 3.89E-06