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 mr1595 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
vg0404517226 sf0404512830 4 4517226 4.32E-08 2.58E-06
vg0810822568 sf0810821573 8 10822568 6.71E-08 6.58E-08
vg0421344282 sf0421172336 4 21344282 4.33E-07 NA
vg0101794928 sf0101793928 1 1794928 2.31E-06 3.79E-06
vg1003557200 sf1003556177 10 3557200 NA 1.70E-06
vg0816279732 sf0816277018 8 16279732 NA 2.73E-06