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 mr1647 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
vg0516615891 sf0516558373 5 16615891 3.83E-07 4.88E-06
vg0516563624 sf0516506106 5 16563624 7.91E-07 1.01E-06
vg0805826839 sf0805825842 8 5826839 9.50E-07 4.02E-06
vg0516784260 sf0516723901 5 16784260 1.29E-06 5.10E-06
vg0709448532 sf0709447538 7 9448532 4.48E-06 2.96E-06
vg0514815080 sf0514757623 5 14815080 NA 3.16E-06