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 mr1563 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
vg0723326000 sf0723325007 7 23326000 1.01E-28 1.54E-19
vg0218947002 sf0218941133 2 18947002 1.01E-11 NA
vg0400455317 sf0400454315 4 455317 1.11E-11 NA
vg0506264380 sf0506264319 5 6264380 2.85E-11 NA
vg0501489854 sf0501489838 5 1489854 2.90E-11 NA
vg0114291290 sf0114290264 1 14291290 NA 2.07E-06