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 mr1290 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
vg0431614108 sf0431429003 4 31614108 8.62E-07 8.62E-07
vg1214822308 sf1214819649 12 14822308 9.30E-07 9.30E-07
vg0431411704 sf0431226602 4 31411704 9.56E-07 9.56E-07
vg0820974361 sf0820971648 8 20974361 1.89E-06 1.89E-06
vg0709984451 sf0709983457 7 9984451 2.28E-06 2.29E-06