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 mr1824 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
vg0915815139 sf0915814138 9 15815139 1.50E-11 2.27E-06
vg1207840077 sf1207837483 12 7840077 6.70E-11 8.25E-07
vg0726964336 sf0726963342 7 26964336 6.82E-11 NA
vg0235046801 sf0235040932 2 35046801 2.69E-10 NA
vg0207696610 sf0207696609 2 7696610 3.26E-10 9.68E-07
vg0805992743 sf0805991746 8 5992743 3.37E-10 1.24E-06
vg0207690117 sf0207690117 2 7690117 1.56E-09 7.40E-07
vg0909309044 sf0909308043 9 9309044 3.75E-09 3.02E-06
vg0921954182 sf0921953701 9 21954182 9.58E-09 9.13E-06
vg0203000556 sf0203000554 2 3000556 2.32E-07 1.48E-06
vg1215167085 sf1215164421 12 15167085 6.87E-07 1.73E-06
vg0432523363 sf0432338255 4 32523363 NA 1.58E-06