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 mr1199 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
vg0719042406 sf0719041413 7 19042406 9.18E-10 1.44E-08
vg0718994741 sf0718993748 7 18994741 1.85E-08 2.59E-08
vg1207833484 sf1207830890 12 7833484 3.27E-08 4.30E-08
vg0900606900 sf0900605900 9 606900 7.29E-07 3.06E-06
vg1210333331 sf1210330744 12 10333331 9.42E-06 4.92E-06