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 mr1230 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
vg0431515534 sf0431330433 4 31515534 2.05E-07 2.47E-06
vg1214822308 sf1214819649 12 14822308 1.09E-06 7.53E-07
vg0142106675 sf0142105632 1 42106675 2.63E-06 9.89E-06
vg0820948405 sf0820945692 8 20948405 5.46E-06 2.85E-06
vg1215354383 sf1215351681 12 15354383 NA 7.35E-06