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 mr1298 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
vg0906682620 sf0906681620 9 6682620 6.04E-09 5.49E-07
vg0223170170 sf0223164301 2 23170170 1.02E-07 4.66E-07
vg1214727671 sf1214725012 12 14727671 2.28E-06 NA
vg1125768032 sf1125301871 11 25768032 3.39E-06 8.43E-07
vg0921099453 sf0921098972 9 21099453 8.24E-06 1.72E-06