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 mr1564 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
vg1117141200 sf1116675052 11 17141200 3.87E-07 5.66E-06
vg0324327479 sf0324325558 3 24327479 7.75E-07 4.52E-06
vg0315952781 sf0315951428 3 15952781 1.14E-06 1.43E-06
vg0225078741 sf0225072872 2 25078741 1.32E-06 NA
vg0419203669 sf0419031705 4 19203669 9.58E-06 NA