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 mr1840 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
vg0918774898 sf0918773898 9 18774898 7.62E-07 7.62E-07
vg0207698155 sf0207698154 2 7698155 1.81E-06 1.81E-06
vg0220358695 sf0220352827 2 20358695 2.21E-06 2.21E-06
vg0916031114 sf0916030113 9 16031114 2.46E-06 2.46E-06
vg0314986971 sf0314985618 3 14986971 2.87E-06 2.87E-06
vg1124277631 sf1123811501 11 24277631 4.78E-06 4.78E-06
vg0509233251 sf0509233180 5 9233251 5.78E-06 5.78E-06