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 mr1232 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
vg0207183259 sf0207183259 2 7183259 8.59E-15 NA
vg0306078536 sf0306077536 3 6078536 1.38E-14 NA
vg1221851164 sf1221817711 12 21851164 1.47E-14 NA
vg0136060970 sf0136059927 1 36060970 1.17E-13 NA
vg1207510234 sf1207507640 12 7510234 1.69E-13 NA
vg1214779581 sf1214776922 12 14779581 2.50E-13 4.15E-06
vg0805968808 sf0805967811 8 5968808 2.77E-12 NA
vg0800333217 sf0800332217 8 333217 2.09E-10 NA
vg1219801760 sf1219773230 12 19801760 2.48E-10 NA
vg0821751104 sf0821748391 8 21751104 1.03E-09 1.98E-06
vg0906525232 sf0906524232 9 6525232 1.60E-09 NA
vg0917594974 sf0917593973 9 17594974 NA 4.48E-06