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 mr1012 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
vg1204159192 sf1204158180 12 4159192 2.63E-08 2.64E-08
vg1224168671 sf1224135125 12 24168671 3.22E-07 3.23E-07
vg0309106481 sf0309105417 3 9106481 7.44E-07 7.47E-07
vg0603070166 sf0603069167 6 3070166 9.32E-07 9.35E-07
vg0816652216 sf0816649502 8 16652216 1.28E-06 1.28E-06
vg0203895379 sf0203895376 2 3895379 2.04E-06 2.05E-06
vg0321930678 sf0321929187 3 21930678 2.22E-06 2.23E-06
vg0816832964 sf0816830250 8 16832964 2.27E-06 2.27E-06
vg0131942064 sf0131941020 1 31942064 2.42E-06 2.43E-06
vg1222561195 sf1222527634 12 22561195 2.67E-06 2.68E-06
vg1210105251 sf1210102662 12 10105251 2.86E-06 2.86E-06
vg0314683652 sf0314682339 3 14683652 2.97E-06 2.99E-06
vg0312184657 sf0312183375 3 12184657 2.98E-06 2.99E-06
vg0406960696 sf0406955964 4 6960696 3.17E-06 3.18E-06
vg0327787353 sf0327780406 3 27787353 3.49E-06 3.50E-06
vg0629559148 sf0629558150 6 29559148 3.92E-06 3.93E-06
vg0215099729 sf0215093859 2 15099729 3.95E-06 3.96E-06
vg1115982226 sf1115517098 11 15982226 4.58E-06 4.59E-06
vg0403320747 sf0403316350 4 3320747 4.77E-06 4.78E-06
vg1124592342 sf1124126182 11 24592342 4.90E-06 4.91E-06