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
vg0714475265 sf0714474272 7 14475265 1.11E-06 1.11E-06
vg1218586541 sf1218557977 12 18586541 1.88E-06 1.88E-06
vg0400169354 sf0400168354 4 169354 2.27E-06 2.27E-06
vg1107363832 sf1107359577 11 7363832 2.64E-06 2.64E-06
vg0231417061 sf0231411192 2 31417061 4.32E-06 4.32E-06
vg0210830120 sf0210830118 2 10830120 4.71E-06 4.71E-06