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 mr1319 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
vg0813739257 sf0813736543 8 13739257 1.53E-07 1.53E-07
vg0414524316 sf0414515030 4 14524316 8.47E-07 8.48E-07
vg1103982461 sf1103978363 11 3982461 1.40E-06 1.40E-06
vg0315249285 sf0315247932 3 15249285 2.10E-06 2.11E-06
vg1222295790 sf1222262337 12 22295790 2.34E-06 2.34E-06
vg0433017442 sf0432832328 4 33017442 2.72E-06 2.72E-06
vg1209904708 sf1209902118 12 9904708 3.07E-06 3.07E-06
vg0405067515 sf0405062954 4 5067515 3.12E-06 3.12E-06
vg0408057625 sf0408052897 4 8057625 3.41E-06 3.42E-06