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 mr1169 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
vg0429941180 sf0429756047 4 29941180 1.49E-26 2.39E-10
vg0429993160 sf0429808027 4 29993160 4.04E-26 1.34E-10
vg0315318288 sf0315316935 3 15318288 1.19E-17 NA
vg0430365268 sf0430180145 4 30365268 2.55E-17 NA
vg0431430004 sf0431244902 4 31430004 2.28E-16 NA
vg0423314049 sf0423128904 4 23314049 3.44E-16 NA
vg0223246090 sf0223240221 2 23246090 NA 8.42E-08
vg0729605765 sf0729604773 7 29605765 NA 2.33E-06
vg1217708323 sf1217702278 12 17708323 NA 3.45E-06
vg1204578962 sf1204577950 12 4578962 NA 4.77E-06