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 mr1013 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
vg0433918375 sf0433733272 4 33918375 1.81E-13 7.21E-10
vg1208472138 sf1208469545 12 8472138 1.02E-11 NA
vg0529082765 sf0529020120 5 29082765 7.50E-11 NA
vg0113480569 sf0113479543 1 13480569 7.65E-11 7.26E-06
vg0304178129 sf0304177131 3 4178129 8.74E-11 NA
vg1017986001 sf1017914773 10 17986001 4.99E-09 2.87E-06
vg0224787316 sf0224781447 2 24787316 2.83E-08 2.44E-06
vg0433939228 sf0433754124 4 33939228 NA 2.20E-06