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 mr1465 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
vg0622492754 sf0622491757 6 22492754 5.67E-08 5.67E-08
vg0625656832 sf0625655835 6 25656832 1.30E-06 1.30E-06
vg0805661208 sf0805660211 8 5661208 1.36E-06 1.36E-06
vg0624389041 sf0624388044 6 24389041 2.09E-06 2.09E-06
vg0630793825 sf0630792827 6 30793825 2.34E-06 2.34E-06
vg0225258286 sf0225252417 2 25258286 3.27E-06 3.27E-06
vg0401981253 sf0401976849 4 1981253 3.63E-06 3.63E-06