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 mr1762 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
vg0434828117 sf0434643008 4 34828117 3.74E-11 5.43E-06
vg0434836925 sf0434651816 4 34836925 4.50E-11 4.01E-06
vg0528509683 sf0528447038 5 28509683 6.87E-11 NA
vg0315255092 sf0315253739 3 15255092 7.48E-11 NA
vg0701136340 sf0701135340 7 1136340 9.01E-11 NA
vg1013286350 sf1013215119 10 13286350 1.78E-10 NA
vg0626508986 sf0626507989 6 26508986 5.58E-10 NA
vg0908960679 sf0908959678 9 8960679 7.42E-07 3.18E-06
vg0208759843 sf0208759842 2 8759843 8.36E-07 5.40E-06
vg0726451328 sf0726450334 7 26451328 1.22E-06 3.15E-06
vg0208262087 sf0208262086 2 8262087 1.75E-06 2.31E-06
vg0907763143 sf0907762143 9 7763143 NA 4.08E-06
vg0725923029 sf0725922035 7 25923029 NA 8.48E-06