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 mr1485 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
vg0819603039 sf0819600326 8 19603039 1.05E-07 1.05E-07
vg0215515811 sf0215509941 2 15515811 2.85E-07 2.85E-07
vg1209961444 sf1209958854 12 9961444 1.23E-06 1.23E-06
vg0726964336 sf0726963342 7 26964336 1.29E-06 1.29E-06
vg0122971893 sf0122970849 1 22971893 1.79E-06 1.79E-06
vg0714622950 sf0714621957 7 14622950 4.35E-06 4.35E-06