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 mr1985 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
vg0138706549 sf0138705506 1 38706549 1.98E-07 1.98E-07
vg0805900956 sf0805899959 8 5900956 4.89E-07 4.89E-07
vg0324965295 sf0324963375 3 24965295 1.59E-06 1.59E-06
vg0805160234 sf0805159237 8 5160234 2.82E-06 2.82E-06
vg1214703763 sf1214701104 12 14703763 3.77E-06 3.78E-06
vg0810507145 sf0810506149 8 10507145 4.30E-06 4.30E-06
vg0403709681 sf0403705287 4 3709681 4.57E-06 4.57E-06