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 mr1909 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
vg0205292202 sf0205292200 2 5292202 2.01E-11 4.09E-09
vg1104966222 sf1104962033 11 4966222 1.26E-08 NA
vg0726964336 sf0726963342 7 26964336 3.43E-08 NA
vg0130736864 sf0130735820 1 30736864 5.19E-08 NA
vg0125460621 sf0125459577 1 25460621 6.55E-08 NA
vg0431411704 sf0431226602 4 31411704 9.24E-08 1.31E-06
vg0207854825 sf0207854824 2 7854825 1.08E-07 4.47E-06
vg1124078478 sf1123612348 11 24078478 1.09E-07 5.69E-08
vg0300249514 sf0300248514 3 249514 9.47E-07 8.49E-06
vg0709984451 sf0709983457 7 9984451 1.17E-06 6.44E-06
vg1115066964 sf1114603278 11 15066964 5.98E-06 2.62E-06
vg0816981965 sf0816979251 8 16981965 NA 8.50E-06