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 mr1153 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
vg0315321037 sf0315319684 3 15321037 3.36E-09 6.24E-06
vg0317301865 sf0317300675 3 17301865 1.46E-08 NA
vg0432158590 sf0431973483 4 32158590 2.44E-08 4.95E-06
vg1013275525 sf1013204295 10 13275525 4.38E-08 NA
vg0321402616 sf0321401126 3 21402616 4.44E-08 NA