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 mr1181 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
vg0402256119 sf0402251714 4 2256119 2.02E-08 4.35E-06
vg0223853067 sf0223847198 2 23853067 3.18E-08 NA
vg0715684046 sf0715683053 7 15684046 3.64E-08 5.93E-06
vg0110547989 sf0110546965 1 10547989 8.78E-08 NA
vg0715691039 sf0715690046 7 15691039 1.85E-07 NA
vg1104315941 sf1104311843 11 4315941 4.26E-07 9.76E-06
vg0414330196 sf0414320909 4 14330196 4.14E-06 NA
vg0910945155 sf0910944154 9 10945155 NA 3.00E-06