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 mr1713 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
vg1019343853 sf1019272408 10 19343853 1.45E-08 2.17E-06
vg0725341761 sf0725340767 7 25341761 7.91E-08 NA
vg0501807593 sf0501807576 5 1807593 2.56E-07 3.01E-06
vg1117292780 sf1116826632 11 17292780 1.02E-06 NA
vg1207457491 sf1207454897 12 7457491 2.74E-06 8.59E-06
vg0434562918 sf0434377810 4 34562918 3.06E-06 1.39E-06