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 mr1879 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
vg0311686305 sf0311685023 3 11686305 1.68E-17 NA
vg0330738629 sf0330731516 3 30738629 9.89E-16 NA
vg0728463202 sf0728462210 7 28463202 1.48E-15 2.44E-06
vg0528187064 sf0528124419 5 28187064 2.69E-15 NA
vg0305768566 sf0305767566 3 5768566 6.86E-15 NA
vg0433674026 sf0433488909 4 33674026 1.23E-12 NA