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 mr1313 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
vg0403709681 sf0403705287 4 3709681 3.67E-09 3.67E-09
vg0805900956 sf0805899959 8 5900956 5.04E-07 5.04E-07
vg0207676313 sf0207676313 2 7676313 5.64E-07 5.64E-07
vg0138706549 sf0138705506 1 38706549 7.98E-07 7.98E-07
vg0407067342 sf0407062613 4 7067342 1.35E-06 1.35E-06
vg1221128182 sf1221094732 12 21128182 3.01E-06 3.01E-06