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 mr1762 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
vg0119166872 sf0119165827 1 19166872 1.44E-07 1.44E-07
vg0119308289 sf0119307244 1 19308289 3.22E-07 3.22E-07
vg0120248259 sf0120247214 1 20248259 1.09E-06 1.09E-06
vg0208411217 sf0208411216 2 8411217 1.13E-06 1.13E-06
vg0726451328 sf0726450334 7 26451328 2.01E-06 2.01E-06
vg0819736179 sf0819733466 8 19736179 2.39E-06 2.39E-06
vg0313073263 sf0313071981 3 13073263 3.69E-06 3.69E-06
vg0217682883 sf0217677013 2 17682883 4.10E-06 4.10E-06
vg0715040944 sf0715039951 7 15040944 7.99E-06 7.99E-06