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 mr1864 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
vg0919435015 sf0919434605 9 19435015 4.08E-13 NA
vg0223256974 sf0223251105 2 23256974 6.38E-13 NA
vg0603392608 sf0603391609 6 3392608 1.14E-12 NA
vg0111064053 sf0111063029 1 11064053 1.18E-12 NA
vg0528968267 sf0528905622 5 28968267 2.03E-12 NA
vg0517640242 sf0517579884 5 17640242 6.04E-11 NA
vg0805645286 sf0805644289 8 5645286 6.44E-10 7.40E-06
vg0901536604 sf0901535604 9 1536604 NA 2.60E-06
vg0804905723 sf0804904726 8 4905723 NA 4.48E-06
vg1226541718 sf1226508113 12 26541718 NA 4.97E-06