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 mr1214 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
vg1117584893 sf1117118750 11 17584893 8.32E-08 1.69E-06
vg0318828127 sf0318826887 3 18828127 1.02E-07 1.81E-06
vg0132003886 sf0132002842 1 32003886 1.25E-07 3.00E-06
vg0910735818 sf0910734817 9 10735818 1.44E-07 6.70E-07
vg0910734707 sf0910733706 9 10734707 3.05E-06 7.77E-07
vg0820422849 sf0820420136 8 20422849 4.04E-06 3.93E-06
vg0910486271 sf0910485270 9 10486271 NA 3.35E-06
vg0610634320 sf0610633321 6 10634320 NA 8.98E-06