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 mr1260 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
vg0232697844 sf0232691975 2 32697844 8.23E-24 NA
vg1110304932 sf1110299509 11 10304932 9.57E-23 NA
vg0719010660 sf0719009667 7 19010660 1.66E-21 NA
vg0610556297 sf0610555298 6 10556297 2.16E-21 NA
vg1010756759 sf1010685580 10 10756759 2.82E-21 NA
vg1105199198 sf1105195009 11 5199198 6.17E-18 NA
vg0234438617 sf0234432748 2 34438617 2.51E-17 NA
vg0141751270 sf0141750227 1 41751270 6.72E-17 NA
vg0323939684 sf0323937858 3 23939684 2.69E-16 NA
vg0129748799 sf0129747754 1 29748799 NA 2.32E-07
vg0114201104 sf0114200078 1 14201104 NA 3.41E-06
vg0810529886 sf0810528890 8 10529886 NA 3.51E-06
vg0233659284 sf0233653415 2 33659284 NA 3.69E-06