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 mr1781 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
vg0404394612 sf0404390216 4 4394612 4.40E-07 4.40E-07
vg0726583792 sf0726582798 7 26583792 1.13E-06 1.13E-06
vg0225887862 sf0225881993 2 25887862 3.96E-06 3.96E-06
vg1207231830 sf1207229226 12 7231830 4.75E-06 4.75E-06
vg1006268134 sf1006283757 10 6268134 8.65E-06 8.65E-06