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 mr1655 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
vg0709448532 sf0709447538 7 9448532 1.56E-07 1.89E-07
vg0516612412 sf0516554894 5 16612412 2.16E-07 3.13E-06
vg0516563624 sf0516506106 5 16563624 5.74E-07 5.51E-07
vg0714179494 sf0714178501 7 14179494 6.36E-07 8.51E-07
vg1022689593 sf1022618067 10 22689593 8.54E-07 3.91E-06
vg0419845320 sf0419673356 4 19845320 3.57E-06 NA
vg1208375941 sf1208373347 12 8375941 6.84E-06 5.56E-07