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 mr1488 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
vg0141835472 sf0141834429 1 41835472 1.42E-10 NA
vg0902107236 sf0902106236 9 2107236 1.96E-10 1.12E-06
vg0528836237 sf0528773592 5 28836237 2.11E-10 9.48E-06
vg0801628860 sf0801627862 8 1628860 2.59E-10 NA
vg0915815139 sf0915814138 9 15815139 3.78E-10 8.93E-06
vg0805992743 sf0805991746 8 5992743 9.69E-10 7.78E-06
vg0433184965 sf0432999853 4 33184965 4.18E-08 NA
vg1219570780 sf1219542250 12 19570780 2.95E-07 NA
vg1214134657 sf1214131997 12 14134657 NA 3.52E-06