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 mr1741 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
vg1123455671 sf1122989541 11 23455671 3.50E-08 NA
vg0414176026 sf0414166742 4 14176026 3.73E-08 4.14E-06
vg0314648455 sf0314647142 3 14648455 6.28E-08 NA
vg0425552229 sf0425367089 4 25552229 6.57E-08 NA
vg0420802623 sf0420630666 4 20802623 7.86E-08 NA
vg0419568634 sf0419396669 4 19568634 4.60E-06 7.91E-06