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 mr1637 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
vg0114147236 sf0114146210 1 14147236 4.27E-08 1.23E-06
vg0414583385 sf0414574099 4 14583385 8.11E-08 NA
vg1207863655 sf1207861061 12 7863655 9.31E-08 7.93E-08
vg0114056307 sf0114055281 1 14056307 8.22E-06 6.56E-06
vg0412619214 sf0412609924 4 12619214 NA 4.27E-06