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 mr1447 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
vg0130736864 sf0130735820 1 30736864 4.21E-08 9.01E-06
vg0300249514 sf0300248514 3 249514 2.52E-07 6.39E-07
vg0130290451 sf0130289406 1 30290451 3.03E-07 NA
vg0514011016 sf0513953560 5 14011016 4.45E-07 5.52E-07
vg0802944461 sf0802943464 8 2944461 5.36E-07 2.49E-06
vg0820796944 sf0820794231 8 20796944 1.02E-06 1.56E-06
vg0118432044 sf0118430998 1 18432044 5.37E-06 NA