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 mr1203 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
vg0406519287 sf0406514730 4 6519287 3.04E-21 1.05E-15
vg0406464503 sf0406459946 4 6464503 2.29E-20 1.41E-14
vg1016565386 sf1016494159 10 16565386 2.69E-10 1.79E-06
vg0619685778 sf0619684781 6 19685778 6.60E-09 2.31E-06
vg0505202290 sf0505202268 5 5202290 2.32E-08 NA
vg0722546543 sf0722545550 7 22546543 3.69E-08 7.50E-06
vg0722626782 sf0722625789 7 22626782 7.98E-08 3.97E-06
vg0619717218 sf0619716221 6 19717218 8.83E-08 3.91E-07
vg0911597491 sf0911596490 9 11597491 5.37E-06 2.40E-06