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 mr1704 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
vg0122959519 sf0122958475 1 22959519 2.48E-09 NA
vg0203895649 sf0203895646 2 3895649 5.79E-09 1.43E-06
vg1017210888 sf1017139661 10 17210888 2.06E-08 NA
vg0407783729 sf0407778997 4 7783729 2.55E-08 NA
vg0909786798 sf0909785797 9 9786798 7.64E-08 NA
vg1117785196 sf1117319052 11 17785196 1.43E-06 NA
vg0207929583 sf0207929582 2 7929583 NA 2.28E-06