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 mr1856 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
vg0819852820 sf0819850107 8 19852820 6.77E-10 1.19E-07
vg0819603039 sf0819600326 8 19603039 7.76E-10 6.35E-08
vg0726964336 sf0726963342 7 26964336 4.38E-08 NA
vg1104978749 sf1104974560 11 4978749 8.55E-08 NA
vg0127428591 sf0127427547 1 27428591 2.27E-06 1.26E-06
vg0820873126 sf0820870413 8 20873126 2.66E-06 3.76E-06
vg1219448781 sf1219420251 12 19448781 9.35E-06 NA