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 mr1629 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
vg0709099871 sf0709098877 7 9099871 1.44E-10 NA
vg0723791682 sf0723790688 7 23791682 1.50E-10 NA
vg0423892005 sf0423706863 4 23892005 2.10E-10 NA
vg0919713333 sf0919712923 9 19713333 4.36E-10 NA
vg0113550938 sf0113549912 1 13550938 2.58E-09 NA
vg0604025538 sf0604024539 6 4025538 1.27E-07 NA
vg0515641255 sf0515583796 5 15641255 4.70E-06 NA