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 mr1498 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
vg0106693749 sf0106692749 1 6693749 2.86E-46 3.91E-31
vg0317879120 sf0317877902 3 17879120 2.80E-26 2.50E-11
vg0105661905 sf0105660905 1 5661905 4.48E-19 2.40E-10
vg0112795014 sf0112793988 1 12795014 3.14E-16 NA
vg0527265168 sf0527202524 5 27265168 5.79E-16 2.42E-07
vg0103833171 sf0103832171 1 3833171 2.69E-13 8.43E-07
vg0106732224 sf0106731224 1 6732224 2.03E-11 1.40E-11
vg0106463385 sf0106462385 1 6463385 6.29E-11 5.73E-10
vg0106295051 sf0106294051 1 6295051 8.61E-10 8.98E-07
vg0604059961 sf0604058962 6 4059961 3.28E-07 1.56E-06
vg0224094487 sf0224088618 2 24094487 4.39E-07 NA
vg0105632160 sf0105631160 1 5632160 NA 3.70E-06