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 mr1518 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
vg0106977787 sf0106976787 1 6977787 3.38E-13 9.84E-08
vg0600327755 sf0600326755 6 327755 3.36E-11 1.14E-06
vg0827871012 sf0827868298 8 27871012 8.65E-11 4.49E-06
vg0600689387 sf0600688388 6 689387 1.24E-10 5.88E-07
vg0301280405 sf0301279403 3 1280405 2.55E-10 NA
vg0134874866 sf0134873823 1 34874866 9.18E-10 NA
vg0516438728 sf0516381210 5 16438728 6.87E-08 5.82E-07
vg0203898222 sf0203898219 2 3898222 1.66E-06 NA
vg0103247262 sf0103246262 1 3247262 4.04E-06 NA
vg0828204953 sf0828202239 8 28204953 4.56E-06 1.17E-06
vg1223152520 sf1223118980 12 23152520 NA 6.95E-06