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 mr1725 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
vg1107342410 sf1107338155 11 7342410 5.89E-08 6.10E-06
vg0122730371 sf0122729327 1 22730371 8.00E-08 7.07E-06
vg0100783830 sf0100782830 1 783830 6.44E-07 3.66E-06
vg1022537974 sf1022466448 10 22537974 1.07E-06 1.85E-06
vg0402463885 sf0402459483 4 2463885 1.95E-06 NA
vg0116741094 sf0116740068 1 16741094 8.58E-06 5.57E-06