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 mr1470 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
vg0316455753 sf0316454398 3 16455753 6.60E-08 6.60E-08
vg0509233251 sf0509233180 5 9233251 1.91E-07 1.91E-07
vg0805055173 sf0805054176 8 5055173 5.80E-07 5.80E-07
vg0805900956 sf0805899959 8 5900956 2.32E-06 2.32E-06
vg0617070993 sf0617069996 6 17070993 3.30E-06 3.30E-06
vg0127135528 sf0127134484 1 27135528 3.43E-06 3.43E-06
vg0318307997 sf0318306779 3 18307997 4.47E-06 4.47E-06
vg0410692283 sf0410682985 4 10692283 4.48E-06 4.48E-06
vg0228320179 sf0228314310 2 28320179 4.91E-06 4.92E-06