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 mr1806 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
vg0716888581 sf0716887588 7 16888581 1.25E-07 1.25E-07
vg0620421679 sf0620420682 6 20421679 1.61E-07 1.61E-07
vg0101205552 sf0101204552 1 1205552 7.04E-07 7.04E-07
vg0717479191 sf0717478198 7 17479191 1.03E-06 1.03E-06
vg0804309408 sf0804308411 8 4309408 2.03E-06 2.03E-06
vg0528218584 sf0528155939 5 28218584 3.84E-06 3.84E-06