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 mr1747 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
vg0819603039 sf0819600326 8 19603039 1.57E-07 1.57E-07
vg0819356506 sf0819353793 8 19356506 2.03E-07 2.03E-07
vg0820873126 sf0820870413 8 20873126 1.50E-06 1.50E-06
vg0621412586 sf0621411589 6 21412586 2.41E-06 2.41E-06
vg0819985140 sf0819982427 8 19985140 2.45E-06 2.45E-06
vg0127428591 sf0127427547 1 27428591 4.94E-06 4.93E-06
vg0122125670 sf0122124625 1 22125670 6.59E-06 6.58E-06