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 mr1449 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
vg0729650535 sf0729649543 7 29650535 7.40E-09 8.36E-06
vg0518964664 sf0518902148 5 18964664 1.62E-08 5.39E-06
vg0404520455 sf0404516058 4 4520455 4.95E-08 6.79E-06
vg0804887405 sf0804886408 8 4887405 5.42E-08 1.37E-06
vg0136579184 sf0136578141 1 36579184 7.90E-08 NA
vg0910968947 sf0910967946 9 10968947 6.98E-07 4.80E-06
vg0800580156 sf0800579156 8 580156 6.36E-06 8.56E-06