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 mr1371 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
vg0122798728 sf0122797684 1 22798728 5.40E-08 1.85E-06
vg0114539569 sf0114538543 1 14539569 5.47E-07 8.09E-07
vg0206101217 sf0206101217 2 6101217 6.25E-06 NA
vg0911386408 sf0911385407 9 11386408 6.30E-06 2.02E-06
vg0820694826 sf0820692113 8 20694826 9.80E-06 3.65E-06