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 mr1741 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
vg0500152728 sf0500152728 5 152728 2.68E-07 9.16E-06
vg1107331327 sf1107327072 11 7331327 7.89E-07 4.79E-06
vg0103304407 sf0103303407 1 3304407 2.38E-06 3.70E-06
vg1002030590 sf1002029567 10 2030590 2.87E-06 2.62E-06
vg1109529411 sf1109523988 11 9529411 4.04E-06 2.81E-06