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 mr1313 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
vg0230805438 sf0230799569 2 30805438 1.48E-07 1.48E-07
vg0626920669 sf0626919672 6 26920669 2.86E-07 2.86E-07
vg0228241702 sf0228235833 2 28241702 8.94E-07 8.95E-07
vg0907583714 sf0907582714 9 7583714 2.14E-06 2.14E-06
vg0801575988 sf0801574990 8 1575988 4.96E-06 4.96E-06