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 mr1497 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
vg0220464869 sf0220459001 2 20464869 7.92E-07 7.92E-07
vg0517989677 sf0517929163 5 17989677 1.12E-06 1.12E-06
vg0620184702 sf0620183705 6 20184702 1.58E-06 1.58E-06
vg0220304760 sf0220298892 2 20304760 1.86E-06 1.86E-06
vg1106197980 sf1106193732 11 6197980 2.79E-06 2.79E-06
vg0918787679 sf0918786679 9 18787679 4.57E-06 4.57E-06