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 mr1364 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
vg0111315642 sf0111314618 1 11315642 6.91E-09 1.37E-07
vg0130385284 sf0130384240 1 30385284 1.18E-08 NA
vg0134514532 sf0134513489 1 34514532 3.01E-08 NA
vg0139586562 sf0139585519 1 39586562 4.09E-08 NA
vg0508127869 sf0508127809 5 8127869 5.14E-08 NA
vg1208976538 sf1208973946 12 8976538 3.01E-07 2.04E-06
vg1209223420 sf1209220829 12 9223420 5.13E-07 NA
vg0414329989 sf0414320702 4 14329989 3.77E-06 NA
vg0225787481 sf0225781612 2 25787481 NA 2.12E-06
vg0403407500 sf0403403103 4 3407500 NA 2.31E-06
vg0402977601 sf0402973207 4 2977601 NA 3.27E-06