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 mr1302 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
vg0208850397 sf0208850395 2 8850397 5.61E-12 NA
vg0618125425 sf0618124428 6 18125425 1.57E-11 NA
vg1219399882 sf1219371352 12 19399882 2.31E-11 NA
vg0212831518 sf0212831514 2 12831518 2.65E-11 NA
vg0916428508 sf0916427507 9 16428508 3.30E-11 NA
vg1215653812 sf1215651109 12 15653812 8.27E-09 3.99E-06
vg0313174041 sf0313172759 3 13174041 1.64E-08 1.43E-06