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 mr1538 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
vg0137881242 sf0137880199 1 37881242 1.05E-18 9.92E-15
vg1122139380 sf1121673251 11 22139380 7.75E-10 5.04E-08
vg1122139627 sf1121673498 11 22139627 1.23E-09 7.17E-08
vg1121710869 sf1121244746 11 21710869 2.40E-09 1.67E-08
vg0709670800 sf0709669806 7 9670800 1.55E-08 2.87E-06
vg0138717572 sf0138716529 1 38717572 2.86E-08 NA
vg1122375122 sf1121908993 11 22375122 3.74E-08 3.09E-06
vg1108338451 sf1108333061 11 8338451 4.00E-08 NA
vg0135705062 sf0135704019 1 35705062 1.25E-07 4.40E-06
vg0918882956 sf0918881956 9 18882956 1.80E-07 4.84E-06
vg1122427075 sf1121960946 11 22427075 3.90E-06 2.76E-06