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 mr1136 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
vg0420836689 sf0420664732 4 20836689 3.53E-09 3.68E-06
vg0423535582 sf0423350439 4 23535582 5.31E-09 5.26E-06
vg0113945497 sf0113944471 1 13945497 2.42E-08 3.83E-06
vg0715472268 sf0715471275 7 15472268 7.20E-08 NA
vg1014161943 sf1014090709 10 14161943 3.19E-07 4.18E-08
vg0405464016 sf0405459457 4 5464016 9.64E-07 NA
vg1005174294 sf1005190831 10 5174294 1.47E-06 2.84E-06
vg0402676745 sf0402672349 4 2676745 1.68E-06 1.03E-06
vg0501181190 sf0501181174 5 1181190 2.83E-06 NA
vg1121617772 sf1121151649 11 21617772 NA 2.90E-06
vg0230571236 sf0230565367 2 30571236 NA 3.79E-06