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 mr1328 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
vg1012367119 sf1012295934 10 12367119 1.83E-10 2.24E-07
vg1012428033 sf1012356848 10 12428033 3.84E-10 7.70E-08
vg0431530955 sf0431345854 4 31530955 5.68E-08 NA
vg0820694826 sf0820692113 8 20694826 1.06E-07 3.96E-07
vg0224478551 sf0224472682 2 24478551 2.28E-07 8.45E-07
vg0434330680 sf0434145574 4 34330680 7.76E-07 3.26E-06