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 mr1930 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
vg0330774928 sf0330767815 3 30774928 1.69E-07 1.95E-06
vg0209213036 sf0209213034 2 9213036 2.68E-07 2.40E-06
vg0525590152 sf0525527573 5 25590152 1.21E-06 3.42E-06
vg1218769925 sf1218741360 12 18769925 2.92E-06 NA
vg0514453158 sf0514395701 5 14453158 4.58E-06 9.73E-06
vg1004625214 sf1004641752 10 4625214 8.74E-06 6.33E-06