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 mr1217 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
vg0433638267 sf0433453150 4 33638267 1.31E-07 1.31E-07
vg0103396097 sf0103395097 1 3396097 2.86E-07 2.86E-07
vg1214822308 sf1214819649 12 14822308 7.74E-07 7.74E-07
vg1007900043 sf1007915653 10 7900043 9.53E-07 9.54E-07
vg0431655631 sf0431470524 4 31655631 1.55E-06 1.55E-06
vg0130163180 sf0130162135 1 30163180 1.58E-06 1.58E-06
vg1104978992 sf1104974803 11 4978992 2.79E-06 2.80E-06
vg0129165743 sf0129164698 1 29165743 3.62E-06 3.62E-06
vg0300249514 sf0300248514 3 249514 4.44E-06 4.44E-06
vg0820974361 sf0820971648 8 20974361 4.93E-06 4.93E-06