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 mr1794 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
vg1008474924 sf1008403786 10 8474924 3.45E-17 2.12E-08
vg1006839627 sf1006855250 10 6839627 2.65E-16 2.80E-10
vg0407823910 sf0407819178 4 7823910 4.62E-14 7.25E-07
vg1009515181 sf1009444002 10 9515181 4.68E-14 8.49E-08
vg0407822256 sf0407817524 4 7822256 9.31E-14 9.37E-08
vg1005827029 sf1005843567 10 5827029 3.62E-13 2.99E-07
vg1216843191 sf1216837145 12 16843191 3.89E-13 1.42E-06
vg0908762776 sf0908761775 9 8762776 4.04E-12 NA
vg0407826287 sf0407821555 4 7826287 1.93E-11 2.32E-06
vg0908878056 sf0908877055 9 8878056 2.42E-11 NA
vg0528707749 sf0528645104 5 28707749 3.78E-11 2.01E-06
vg0502157240 sf0502157215 5 2157240 1.20E-10 1.22E-06
vg1216569888 sf1216567181 12 16569888 1.54E-09 2.77E-06