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 mr1694 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
vg1013275525 sf1013204295 10 13275525 9.30E-07 9.30E-07
vg0426278854 sf0426093727 4 26278854 2.01E-06 2.01E-06
vg0224869035 sf0224863166 2 24869035 2.01E-06 2.01E-06
vg0219809349 sf0219803481 2 19809349 2.12E-06 2.13E-06
vg0216351003 sf0216345133 2 16351003 2.38E-06 2.39E-06
vg1017171887 sf1017100659 10 17171887 2.47E-06 2.48E-06
vg0818820911 sf0818818198 8 18820911 3.44E-06 3.44E-06
vg0206274898 sf0206274898 2 6274898 3.62E-06 3.63E-06
vg0304109172 sf0304108168 3 4109172 4.59E-06 4.60E-06
vg0105456852 sf0105455852 1 5456852 4.94E-06 4.95E-06