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 mr1170 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
vg0206233846 sf0206233846 2 6233846 1.33E-12 1.17E-07
vg0206054174 sf0206054174 2 6054174 4.68E-12 4.63E-08
vg1218154919 sf1218126355 12 18154919 1.16E-11 NA
vg0205521492 sf0205521492 2 5521492 5.73E-11 NA
vg0206038889 sf0206038889 2 6038889 6.97E-11 3.78E-07
vg0808932458 sf0808931462 8 8932458 7.89E-11 NA
vg1122506020 sf1122039891 11 22506020 8.16E-11 1.56E-06
vg1122506457 sf1122040328 11 22506457 1.49E-10 1.38E-06
vg0205559811 sf0205559811 2 5559811 5.69E-10 1.79E-06
vg0206232457 sf0206232457 2 6232457 2.50E-08 8.00E-08
vg0224207855 sf0224201986 2 24207855 3.94E-08 2.63E-06
vg1218153472 sf1218124908 12 18153472 2.64E-07 3.62E-06
vg0626387317 sf0626386320 6 26387317 5.62E-06 NA
vg1123045587 sf1122579458 11 23045587 5.82E-06 NA
vg0401702548 sf0401698097 4 1702548 7.17E-06 NA
vg0520863717 sf0520801158 5 20863717 NA 3.11E-06