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 mr1910 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
vg0602313316 sf0602312317 6 2313316 1.43E-10 1.43E-10
vg0219292377 sf0219286509 2 19292377 3.47E-07 3.47E-07
vg0303197045 sf0303196041 3 3197045 6.88E-07 6.88E-07
vg0914711247 sf0914710246 9 14711247 7.79E-07 7.79E-07
vg0221166244 sf0221160376 2 21166244 1.41E-06 1.41E-06
vg0627307052 sf0627306055 6 27307052 2.64E-06 2.64E-06
vg0611333425 sf0611332426 6 11333425 2.79E-06 2.79E-06
vg1119170327 sf1118704015 11 19170327 3.00E-06 3.00E-06
vg0329782503 sf0329775543 3 29782503 3.54E-06 3.54E-06
vg0224549820 sf0224543951 2 24549820 4.45E-06 4.45E-06
vg0716372539 sf0716371546 7 16372539 4.45E-06 4.45E-06