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 mr1664 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
vg1020503467 sf1020431946 10 20503467 1.26E-07 1.26E-07
vg0804453676 sf0804452679 8 4453676 4.46E-07 4.46E-07
vg1220271697 sf1220243139 12 20271697 6.75E-07 6.76E-07
vg0234336153 sf0234330284 2 34336153 8.22E-07 8.23E-07
vg0334841623 sf0334834493 3 34841623 1.40E-06 1.41E-06
vg0903783463 sf0903782463 9 3783463 1.91E-06 1.91E-06
vg0701185368 sf0701184368 7 1185368 2.13E-06 2.13E-06
vg0306112685 sf0306111685 3 6112685 4.97E-06 4.98E-06