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 mr1427 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
vg0706405260 sf0706404265 7 6405260 6.91E-08 6.91E-08
vg1104467562 sf1104463464 11 4467562 3.25E-07 3.25E-07
vg0623014227 sf0623013230 6 23014227 3.53E-07 3.53E-07
vg0420798136 sf0420626179 4 20798136 1.17E-06 1.17E-06
vg0817557507 sf0817554793 8 17557507 1.56E-06 1.56E-06
vg0623981969 sf0623980972 6 23981969 3.83E-06 3.83E-06
vg0501763185 sf0501763168 5 1763185 4.97E-06 4.97E-06