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
vg0222727216 sf0222721347 2 22727216 8.62E-39 4.66E-11
vg0626572977 sf0626571980 6 26572977 2.28E-35 NA
vg0623362787 sf0623361790 6 23362787 4.38E-34 NA
vg0916936193 sf0916935192 9 16936193 9.14E-34 NA
vg0136201965 sf0136200922 1 36201965 6.43E-33 NA
vg0222628680 sf0222622811 2 22628680 NA 6.17E-07
vg0406854976 sf0406850421 4 6854976 NA 2.62E-06