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 mr1952 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
vg1121838431 sf1121372308 11 21838431 1.54E-12 NA
vg0431667654 sf0431482547 4 31667654 3.31E-12 NA
vg0502090757 sf0502090739 5 2090757 3.42E-11 7.58E-06
vg0914466352 sf0914465351 9 14466352 4.35E-11 NA
vg0816013049 sf0816010335 8 16013049 4.52E-11 NA
vg0501779956 sf0501779939 5 1779956 7.35E-11 5.05E-08
vg0517675338 sf0517614979 5 17675338 1.68E-09 NA
vg0420718113 sf0420546156 4 20718113 8.90E-09 4.97E-06
vg0420718198 sf0420546241 4 20718198 6.90E-08 NA
vg0328876399 sf0328869452 3 28876399 3.62E-07 NA
vg0335988697 sf0335981566 3 35988697 5.30E-07 NA
vg0502212455 sf0502212430 5 2212455 NA 1.01E-07
vg0232755756 sf0232749887 2 32755756 NA 9.37E-07
vg0421028434 sf0420856487 4 21028434 NA 1.49E-06