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 mr1682 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
vg0805936415 sf0805935418 8 5936415 4.42E-10 6.40E-09
vg0811907223 sf0811906228 8 11907223 1.86E-08 1.09E-06
vg0206498126 sf0206498126 2 6498126 6.89E-08 NA
vg0405797011 sf0405792450 4 5797011 1.40E-07 4.53E-06
vg0108533994 sf0108532994 1 8533994 1.92E-07 9.16E-07
vg0400963078 sf0400958630 4 963078 2.59E-07 3.25E-06
vg0103158278 sf0103157278 1 3158278 4.77E-07 3.47E-07
vg0824611688 sf0824608974 8 24611688 1.23E-06 3.47E-07
vg0805855827 sf0805854830 8 5855827 1.26E-06 2.02E-06
vg0500444514 sf0500444514 5 444514 4.92E-06 1.24E-06
vg0304703745 sf0304702747 3 4703745 6.48E-06 1.38E-06
vg0905693969 sf0905692969 9 5693969 7.44E-06 6.24E-06
vg0232881115 sf0232875246 2 32881115 NA 2.27E-06
vg0202716112 sf0202716110 2 2716112 NA 2.32E-06
vg1204690369 sf1204689357 12 4690369 NA 3.45E-06