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 mr1767 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
vg0205297301 sf0205297300 2 5297301 6.54E-11 9.74E-08
vg0125460828 sf0125459784 1 25460828 4.11E-09 NA
vg0205039940 sf0205039937 2 5039940 5.34E-09 2.06E-06
vg0300249514 sf0300248514 3 249514 2.54E-08 6.71E-07
vg0726964336 sf0726963342 7 26964336 4.14E-08 NA
vg0711746376 sf0711745382 7 11746376 6.19E-06 2.47E-06