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 mr1057 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
vg0105144997 sf0105143997 1 5144997 1.14E-25 3.13E-20
vg0810146037 sf0810145041 8 10146037 1.23E-11 NA
vg0207379019 sf0207379019 2 7379019 2.68E-11 1.77E-06
vg0810144928 sf0810143932 8 10144928 4.26E-11 2.23E-06
vg0918927566 sf0918926566 9 18927566 6.79E-10 NA
vg1220853596 sf1220820145 12 20853596 8.00E-10 NA
vg0810065977 sf0810064981 8 10065977 9.76E-10 1.62E-06
vg0820260559 sf0820257846 8 20260559 8.54E-07 NA
vg0105151694 sf0105150694 1 5151694 NA 1.79E-06
vg0104750274 sf0104749274 1 4750274 NA 1.96E-06