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 mr1784 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
vg0821751104 sf0821748391 8 21751104 4.60E-08 NA
vg0220095539 sf0218482837 2 20095539 5.12E-08 NA
vg0820888052 sf0820885339 8 20888052 1.43E-06 NA
vg0432523372 sf0432338264 4 32523372 3.65E-06 2.92E-06
vg0432523363 sf0432338255 4 32523363 7.16E-06 5.31E-06
vg1016429449 sf1016358223 10 16429449 NA 4.47E-06