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 mr1627 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
vg0141770822 sf0141769779 1 41770822 5.12E-31 NA
vg0820850557 sf0820847844 8 20850557 1.11E-29 NA
vg0133305720 sf0133304676 1 33305720 1.89E-28 NA
vg0726964336 sf0726963342 7 26964336 2.65E-28 NA
vg0123684776 sf0123683732 1 23684776 7.26E-28 NA
vg0228665356 sf0228659487 2 28665356 NA 6.89E-07
vg0228612339 sf0228606470 2 28612339 NA 8.66E-07
vg0207234669 sf0207234669 2 7234669 NA 9.35E-07
vg0628643421 sf0628642423 6 28643421 NA 3.58E-06
vg0214438331 sf0214432461 2 14438331 NA 3.62E-06