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 mr1838 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
vg0205283916 sf0205283914 2 5283916 1.48E-25 3.51E-08
vg0205285978 sf0205285976 2 5285978 1.97E-25 9.84E-09
vg0726964336 sf0726963342 7 26964336 7.42E-21 NA
vg1102165259 sf1102161117 11 2165259 1.47E-19 NA
vg0138549542 sf0138548499 1 38549542 1.20E-18 NA
vg0306258301 sf0306257301 3 6258301 1.58E-18 NA
vg1101631388 sf1101630389 11 1631388 6.56E-17 NA
vg0517990921 sf0517930407 5 17990921 NA 5.79E-08
vg1214656787 sf1214654127 12 14656787 NA 1.41E-06
vg0819439794 sf0819437081 8 19439794 NA 4.42E-06