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 mr1241 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
vg0311534838 sf0311533556 3 11534838 1.49E-15 NA
vg0719160137 sf0719159144 7 19160137 6.73E-15 5.86E-08
vg0719323752 sf0719322759 7 19323752 1.09E-14 1.61E-08
vg0604329275 sf0604328276 6 4329275 2.88E-14 NA
vg0329561125 sf0329554165 3 29561125 5.29E-14 3.65E-06
vg0527267636 sf0527204992 5 27267636 6.47E-14 NA
vg0312702703 sf0312701421 3 12702703 7.99E-14 3.57E-07
vg0421592157 sf0421420207 4 21592157 2.03E-13 1.31E-06
vg1103603230 sf1103599133 11 3603230 1.45E-12 7.28E-07
vg0123367773 sf0123366729 1 23367773 3.87E-12 1.80E-06
vg0435027079 sf0434841967 4 35027079 6.08E-12 3.49E-06
vg1004415668 sf1004432206 10 4415668 NA 5.94E-07
vg1011367434 sf1011296253 10 11367434 NA 1.99E-06
vg1004566041 sf1004582579 10 4566041 NA 5.08E-06