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 mr1679 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
vg0114039871 sf0114038845 1 14039871 7.09E-10 4.09E-07
vg0113976460 sf0113975434 1 13976460 3.62E-09 5.73E-07
vg1017101445 sf1017030217 10 17101445 1.64E-08 1.17E-06
vg0501460647 sf0501460631 5 1460647 1.93E-08 NA
vg0420836689 sf0420664732 4 20836689 2.02E-08 4.84E-06
vg0327966361 sf0327959415 3 27966361 2.15E-08 NA
vg0500056395 sf0500056395 5 56395 2.72E-08 3.22E-06
vg0327983003 sf0327976057 3 27983003 2.80E-08 NA
vg0207309507 sf0207309507 2 7309507 6.91E-07 3.05E-07
vg0334056878 sf0334049748 3 34056878 1.05E-06 3.30E-06
vg0207312321 sf0207312321 2 7312321 1.24E-06 3.48E-07
vg0620214077 sf0620213080 6 20214077 2.95E-06 4.00E-06
vg1010554538 sf1010483359 10 10554538 NA 9.66E-07