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 mr1957 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
vg0502105278 sf0502105260 5 2105278 3.03E-07 3.03E-07
vg0626058260 sf0626057263 6 26058260 1.85E-06 1.85E-06
vg0521871798 sf0521809240 5 21871798 1.92E-06 1.92E-06
vg1105181691 sf1105177502 11 5181691 1.94E-06 1.94E-06
vg0802234736 sf0802233739 8 2234736 2.69E-06 2.69E-06
vg0217713261 sf0217707391 2 17713261 3.62E-06 3.62E-06
vg0626522332 sf0626521335 6 26522332 3.86E-06 3.86E-06