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 mr1546 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
vg0504932244 sf0504932222 5 4932244 1.48E-08 4.96E-09
vg0413093616 sf0413084326 4 13093616 1.63E-08 1.23E-08
vg0223272315 sf0223266446 2 23272315 2.02E-08 5.61E-07
vg0223115199 sf0223109330 2 23115199 5.55E-08 2.25E-07
vg0512682109 sf0512625031 5 12682109 2.95E-07 1.01E-06
vg0913083924 sf0913082923 9 13083924 3.29E-07 6.65E-07
vg0319618333 sf0319616844 3 19618333 1.65E-06 6.03E-06
vg1022646824 sf1022575298 10 22646824 2.44E-06 2.95E-06
vg0502116989 sf0502116963 5 2116989 2.73E-06 2.32E-06
vg0804076961 sf0804075964 8 4076961 5.95E-06 1.22E-06
vg1103886177 sf1103882079 11 3886177 7.70E-06 9.94E-07
vg0613434230 sf0613433231 6 13434230 NA 3.24E-06
vg0614471183 sf0614470184 6 14471183 NA 4.29E-06