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 mr1035 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
vg0405662754 sf0405658194 4 5662754 1.45E-13 1.22E-10
vg0405667994 sf0405663433 4 5667994 1.67E-13 2.75E-11
vg0408983975 sf0408979251 4 8983975 3.78E-09 4.41E-07
vg0408863993 sf0408859270 4 8863993 7.24E-09 2.78E-07
vg0411444492 sf0411435194 4 11444492 4.19E-08 2.09E-06
vg0806485055 sf0806484060 8 6485055 5.15E-08 NA
vg0405169454 sf0405164896 4 5169454 5.08E-07 2.13E-06
vg0406062876 sf0406058315 4 6062876 1.12E-06 1.67E-07