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 mr1471 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
vg0335609544 sf0335602413 3 35609544 2.59E-08 9.73E-07
vg0904833561 sf0904832561 9 4833561 4.95E-08 1.07E-06
vg0620734924 sf0620733927 6 20734924 3.12E-07 3.23E-07
vg0906206648 sf0906205648 9 6206648 1.08E-06 9.50E-07
vg0527368492 sf0527305848 5 27368492 2.76E-06 2.69E-06
vg0906163068 sf0906162068 9 6163068 5.49E-06 NA
vg0114152314 sf0114151288 1 14152314 NA 3.21E-07