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 mr1171 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
vg1218731515 sf1218702950 12 18731515 4.28E-08 8.33E-07
vg0208158153 sf0208158152 2 8158153 2.53E-07 2.15E-06
vg0207884913 sf0207884912 2 7884913 6.41E-07 1.88E-06
vg0208190322 sf0208190321 2 8190322 1.21E-06 4.89E-06
vg0223419823 sf0223413954 2 23419823 5.62E-06 4.26E-06
vg1218012774 sf1217984210 12 18012774 8.50E-06 NA