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 mr1229 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
vg0217838858 sf0217832989 2 17838858 7.22E-10 1.05E-07
vg0217259650 sf0217253780 2 17259650 3.31E-09 9.55E-08
vg1114596701 sf1114133019 11 14596701 8.44E-09 7.62E-07
vg0610866929 sf0610865930 6 10866929 6.57E-07 2.78E-06
vg1214822308 sf1214819649 12 14822308 8.92E-06 NA