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 mr1587 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
vg0909074795 sf0909073794 9 9074795 5.08E-07 5.08E-07
vg1214780957 sf1214778298 12 14780957 8.18E-07 8.18E-07
vg0219886046 sf0219880178 2 19886046 8.46E-07 8.46E-07
vg1120641607 sf1120175528 11 20641607 1.25E-06 1.25E-06
vg1003824713 sf1003823689 10 3824713 1.79E-06 1.79E-06
Unknow sf1128497993 Unknow Unknow 2.49E-06 2.49E-06
vg1214995396 sf1214992738 12 14995396 3.34E-06 3.34E-06
vg0329626503 sf0329619543 3 29626503 4.04E-06 4.04E-06
vg0210784018 sf0210784016 2 10784018 4.82E-06 4.82E-06
vg0522330048 sf0522267489 5 22330048 4.97E-06 4.98E-06