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 mr1746 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
vg0800213505 sf0800212505 8 213505 1.43E-28 3.24E-21
vg0800287831 sf0800286831 8 287831 3.96E-28 2.23E-21
vg0800302779 sf0800301779 8 302779 5.98E-24 4.97E-20
vg0800213386 sf0800212386 8 213386 2.60E-19 1.03E-16
vg0800452763 sf0800451763 8 452763 2.46E-12 1.71E-08
vg0800347061 sf0800346061 8 347061 1.19E-08 1.02E-06
vg0622463129 sf0622462132 6 22463129 2.81E-08 3.87E-06
vg0622302006 sf0622301009 6 22302006 4.15E-08 7.96E-07
vg0800085930 sf0800084930 8 85930 7.45E-08 2.08E-06
vg0800402121 sf0800401121 8 402121 7.72E-07 1.92E-06
vg0817248199 sf0817245485 8 17248199 2.32E-06 4.50E-07
vg1122447657 sf1121981528 11 22447657 8.38E-06 NA
vg0812794506 sf0812792331 8 12794506 NA 2.31E-06