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 mr1862 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
vg1018583557 sf1018512114 10 18583557 2.36E-09 2.20E-06
vg1018632917 sf1018561474 10 18632917 6.56E-09 1.99E-06
vg0821751104 sf0821748391 8 21751104 5.03E-08 NA
vg0820422849 sf0820420136 8 20422849 1.35E-07 4.57E-06
vg1214822308 sf1214819649 12 14822308 1.38E-07 1.41E-06
vg1219590404 sf1219561874 12 19590404 9.75E-06 NA