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 mr1928 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
vg0142373682 sf0142372638 1 42373682 3.24E-10 NA
vg0224958355 sf0224952486 2 24958355 2.84E-08 NA
vg1021644818 sf1021573295 10 21644818 1.26E-07 NA
vg1118447476 sf1117981335 11 18447476 6.50E-06 3.64E-06
vg0307269169 sf0307268167 3 7269169 NA 2.64E-06
vg0307254492 sf0307253490 3 7254492 NA 3.19E-06