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 mr1477 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
vg0610813941 sf0610812942 6 10813941 1.10E-09 1.10E-09
vg0620435111 sf0620434114 6 20435111 1.16E-09 1.16E-09
vg0616229238 sf0616228240 6 16229238 4.10E-07 4.10E-07
vg0618995622 sf0618994625 6 18995622 4.19E-07 4.19E-07
vg0611846756 sf0611845757 6 11846756 4.51E-07 4.51E-07
vg0400644328 sf0400643327 4 644328 1.07E-06 1.07E-06
vg0619229693 sf0619228696 6 19229693 2.92E-06 2.92E-06
vg1109865369 sf1109859946 11 9865369 3.16E-06 3.16E-06
vg0619155351 sf0619154354 6 19155351 4.77E-06 4.77E-06