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 mr1332 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
vg0219483986 sf0219478118 2 19483986 8.61E-08 3.33E-07
vg0319113443 sf0319112203 3 19113443 1.91E-07 4.63E-06
vg1124474541 sf1124008381 11 24474541 6.58E-07 3.72E-06
vg0729463054 sf0729462062 7 29463054 9.78E-07 3.02E-06
vg0141090615 sf0141089572 1 41090615 2.12E-06 NA