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 mr1258 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
vg1207844031 sf1207841437 12 7844031 5.62E-07 5.59E-07
vg1022934549 sf1022863021 10 22934549 1.21E-06 1.21E-06
vg0406040035 sf0406035474 4 6040035 2.07E-06 2.08E-06
vg1105740618 sf1105736370 11 5740618 2.93E-06 2.95E-06
vg1022900912 sf1022829384 10 22900912 3.10E-06 3.12E-06
vg0105514893 sf0105513893 1 5514893 3.18E-06 3.19E-06
vg0622630936 sf0622629939 6 22630936 3.39E-06 3.40E-06