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 mr1555 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
vg0128530606 sf0128529561 1 28530606 2.50E-10 8.10E-07
vg1206398865 sf1206397755 12 6398865 8.96E-10 9.51E-07
vg0402458323 sf0402453921 4 2458323 1.77E-09 NA
vg1210467503 sf1210464916 12 10467503 2.85E-09 NA
vg0812660312 sf0812658137 8 12660312 7.22E-09 NA
vg0402163681 sf0402159276 4 2163681 8.65E-09 4.79E-06
vg0223422615 sf0223416746 2 23422615 1.38E-08 4.80E-06
vg0317321849 sf0317320659 3 17321849 2.35E-08 3.02E-06
vg0608150754 sf0608149755 6 8150754 1.43E-07 2.27E-06
vg0421031221 sf0420859274 4 21031221 3.53E-06 3.51E-06
vg0605513869 sf0605512870 6 5513869 NA 3.10E-07
vg0808431807 sf0808430811 8 8431807 NA 1.33E-06