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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 mr1256 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
vg1213938478 sf1213940524 12 13938478 1.13E-06 1.13E-06
vg0320549807 sf0320548318 3 20549807 1.60E-06 1.60E-06
vg1213938463 sf1213940509 12 13938463 3.03E-06 3.03E-06
vg0318001497 sf0318000279 3 18001497 3.22E-06 3.22E-06
vg0608860294 sf0608859295 6 8860294 3.57E-06 3.57E-06