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 mr1136 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
vg1226578493 sf1226544888 12 26578493 4.33E-09 5.26E-06
vg1213285645 sf1213282983 12 13285645 7.66E-09 2.20E-06
vg1001679807 sf1001678784 10 1679807 6.16E-08 NA
vg0404543398 sf0404539001 4 4543398 6.51E-07 6.39E-07
vg0203428396 sf0203428394 2 3428396 NA 4.09E-06