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 mr1049 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
vg0228468795 sf0228462926 2 28468795 4.27E-10 1.38E-07
vg0909829640 sf0909828639 9 9829640 2.41E-08 1.26E-06
vg0519574200 sf0519511684 5 19574200 6.16E-08 NA
vg0816119916 sf0816117202 8 16119916 1.97E-06 1.73E-06
vg1109631523 sf1109626100 11 9631523 6.58E-06 6.93E-07
vg0421023551 sf0420851604 4 21023551 NA 2.40E-06