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 mr1554 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
vg1214346774 sf1214344114 12 14346774 3.49E-09 8.67E-06
vg0420624109 sf0420452152 4 20624109 6.03E-09 4.01E-06
vg0919423685 sf0919423275 9 19423685 1.66E-08 NA
vg1211545082 sf1211542418 12 11545082 1.99E-08 NA
vg0307901966 sf0307900904 3 7901966 2.50E-08 5.65E-06
vg1213717963 sf1213715301 12 13717963 1.81E-07 4.88E-06