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 mr1757 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
vg0421031215 sf0420859268 4 21031215 4.22E-09 6.26E-08
vg0421028117 sf0420856170 4 21028117 6.30E-09 4.66E-08
vg0421302742 sf0421130796 4 21302742 2.09E-06 6.93E-07
vg1108255008 sf1108249618 11 8255008 6.09E-06 3.64E-06
vg0421497689 sf0421325740 4 21497689 8.04E-06 1.28E-06