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 mr1869 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
vg1214822308 sf1214819649 12 14822308 3.43E-08 3.43E-08
vg1104966222 sf1104962033 11 4966222 5.10E-07 5.10E-07
vg0820888052 sf0820885339 8 20888052 8.27E-07 8.27E-07
vg0709984451 sf0709983457 7 9984451 1.69E-06 1.69E-06
vg1217604400 sf1217598355 12 17604400 2.39E-06 2.39E-06
vg1210206055 sf1210203466 12 10206055 3.63E-06 3.63E-06
vg1217776016 sf1217747450 12 17776016 4.22E-06 4.22E-06
vg1219554252 sf1219525722 12 19554252 4.51E-06 4.52E-06