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 mr1401 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
vg0820950016 sf0820947303 8 20950016 3.65E-29 NA
vg0800035708 sf0800034708 8 35708 4.47E-29 NA
vg0624030080 sf0624029083 6 24030080 7.59E-29 NA
vg0311735490 sf0311734208 3 11735490 2.17E-28 NA
vg1220874786 sf1220841335 12 20874786 6.96E-28 NA
vg0820991239 sf0820988526 8 20991239 1.09E-26 5.04E-07
vg1214799373 sf1214796714 12 14799373 3.04E-26 1.11E-07
vg0820948192 sf0820945479 8 20948192 1.84E-25 4.05E-07
vg0805968808 sf0805967811 8 5968808 5.01E-24 6.17E-07
vg0103143509 sf0103142509 1 3143509 2.56E-22 NA
vg0717056152 sf0717055159 7 17056152 NA 6.00E-06