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 mr1409 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
vg0325710457 sf0325708475 3 25710457 7.59E-16 7.94E-14
vg0325696417 sf0325694435 3 25696417 8.53E-16 4.03E-14
vg0400345487 sf0400344487 4 345487 2.33E-11 4.39E-09
vg0609926305 sf0609925306 6 9926305 1.73E-09 7.17E-08
vg1121970827 sf1121504698 11 21970827 3.13E-09 4.66E-07
vg1005318826 sf1005335363 10 5318826 1.12E-08 NA
vg0605613230 sf0605612231 6 5613230 2.73E-08 5.18E-07
vg1005384319 sf1005400856 10 5384319 3.01E-08 5.18E-07
vg1012753141 sf1012681956 10 12753141 5.97E-08 2.82E-06
vg0227974018 sf0227968149 2 27974018 1.34E-07 1.41E-06
vg0415028838 sf0415019552 4 15028838 3.45E-07 7.85E-07
vg0705065736 sf0705064737 7 5065736 9.97E-06 NA