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 mr1193 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
vg0327580115 sf0327573168 3 27580115 1.31E-15 3.03E-09
vg0327580144 sf0327573197 3 27580144 1.21E-14 2.05E-09
vg0327580307 sf0327573360 3 27580307 1.80E-14 1.46E-09
vg0327475017 sf0327468070 3 27475017 3.09E-12 9.70E-08
vg0327476640 sf0327469693 3 27476640 2.12E-11 1.61E-07
vg0114100604 sf0114099578 1 14100604 9.52E-11 3.02E-06
vg0114289453 sf0114288427 1 14289453 9.63E-11 1.44E-07
vg0133299141 sf0133298097 1 33299141 4.38E-09 NA
vg1126262789 sf1125791202 11 26262789 4.79E-09 NA
vg0114279275 sf0114278249 1 14279275 2.59E-08 2.83E-06
vg0112515893 sf0112514867 1 12515893 4.68E-08 3.83E-06
vg0327935681 sf0327928735 3 27935681 7.41E-08 NA
vg0211790176 sf0211790172 2 11790176 1.91E-07 2.44E-07
vg0412701691 sf0412692402 4 12701691 4.07E-07 1.89E-06