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 mr1665 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
vg0805992743 sf0805991746 8 5992743 7.49E-10 3.82E-08
vg0801697883 sf0801696886 8 1697883 9.11E-09 3.35E-07
vg1118023722 sf1117557580 11 18023722 1.26E-08 7.59E-07
vg1020531763 sf1020460242 10 20531763 1.77E-08 4.80E-07
vg0726559146 sf0726558152 7 26559146 1.95E-08 9.57E-07
vg0606329912 sf0606328913 6 6329912 3.39E-08 3.15E-06
vg0335297514 sf0335290383 3 35297514 4.04E-08 1.36E-06
vg0716717405 sf0716716412 7 16717405 8.96E-08 3.49E-06
vg0430475778 sf0430290656 4 30475778 9.49E-08 4.87E-06
vg0630374083 sf0630373085 6 30374083 1.79E-07 2.68E-06
vg0102103204 sf0102102204 1 2103204 3.69E-07 3.50E-06
vg0223525077 sf0223519208 2 23525077 4.48E-07 4.65E-06
vg0113652030 sf0113651004 1 13652030 1.74E-06 3.40E-07
vg0630443303 sf0630442305 6 30443303 NA 1.01E-06
vg0124420479 sf0124419435 1 24420479 NA 3.72E-06
vg0718397736 sf0718396743 7 18397736 NA 4.41E-06