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 mr1740 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
vg0719013107 sf0719012114 7 19013107 9.82E-18 6.09E-06
vg0132153349 sf0132152305 1 32153349 2.35E-17 NA
vg0111937994 sf0111936968 1 11937994 5.35E-17 NA
vg0223425649 sf0223419780 2 23425649 3.51E-16 NA
vg0326901219 sf0326894272 3 26901219 4.02E-16 NA
vg0221140698 sf0221134830 2 21140698 3.43E-15 NA
vg1017902229 sf1017831001 10 17902229 6.62E-14 NA
vg1117484883 sf1117018738 11 17484883 5.10E-13 3.63E-06
vg0429750241 sf0429565110 4 29750241 NA 5.12E-07
vg0406781539 sf0406776984 4 6781539 NA 2.65E-06
vg0210259258 sf0210259256 2 10259258 NA 4.77E-06
vg0630258758 sf0630257760 6 30258758 NA 6.29E-06
vg0519509643 sf0519447127 5 19509643 NA 9.13E-06
vg0808625370 sf0808624374 8 8625370 NA 9.16E-06