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
vg0324965295 sf0324963375 3 24965295 2.99E-07 1.73E-06
vg0805900956 sf0805899959 8 5900956 7.22E-07 3.42E-06
vg0816086900 sf0816084186 8 16086900 8.54E-07 3.90E-06
vg0509233251 sf0509233180 5 9233251 1.17E-06 1.87E-06
vg0223175044 sf0223169175 2 23175044 2.29E-06 NA
vg0901297998 sf0901296998 9 1297998 9.70E-06 NA