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 mr1968 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
vg0718144985 sf0718143992 7 18144985 4.34E-12 5.43E-07
vg0718107292 sf0718106299 7 18107292 5.77E-11 1.99E-07
vg0111174891 sf0111173867 1 11174891 7.97E-11 NA
vg0222612606 sf0222606737 2 22612606 7.85E-10 NA
vg0306403146 sf0306402146 3 6403146 8.68E-10 NA
vg0921121859 sf0921121378 9 21121859 8.82E-10 NA
vg0922167130 sf0922166649 9 22167130 1.69E-09 NA
vg1022039819 sf1021968294 10 22039819 1.28E-08 NA
vg0628631429 sf0628630431 6 28631429 4.86E-06 NA