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 mr1206 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
vg0726847020 sf0726846026 7 26847020 3.17E-07 6.70E-06
vg0431614108 sf0431429003 4 31614108 7.72E-07 5.06E-06
vg1106375766 sf1106371518 11 6375766 1.19E-06 1.60E-06
vg0431655631 sf0431470524 4 31655631 1.37E-06 3.30E-06
vg1219590404 sf1219561874 12 19590404 1.41E-06 2.63E-06
vg0514184495 sf0514127039 5 14184495 1.49E-06 2.65E-06
vg0805469573 sf0805468576 8 5469573 5.17E-06 2.33E-06
vg1124078257 sf1123612127 11 24078257 9.64E-06 3.07E-06
vg1016429449 sf1016358223 10 16429449 NA 3.11E-06