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 mr1571 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
vg0917280218 sf0917279217 9 17280218 1.80E-27 NA
vg1219166608 sf1219138042 12 19166608 3.12E-27 NA
vg0303811213 sf0303810209 3 3811213 4.23E-27 NA
vg1201956134 sf1201960603 12 1956134 7.96E-27 NA
vg0230371738 sf0230365869 2 30371738 1.04E-26 NA
vg0917910484 sf0917909483 9 17910484 1.01E-25 NA
vg0819854080 sf0819851367 8 19854080 1.77E-24 NA
vg0609858987 sf0609857988 6 9858987 NA 2.15E-08
vg0610434106 sf0610433107 6 10434106 NA 6.15E-07
vg1017033032 sf1016961804 10 17033032 NA 7.83E-06