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 mr1850 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
vg0506207863 sf0506207802 5 6207863 4.88E-22 2.82E-15
vg0502976477 sf0502976453 5 2976477 1.24E-19 2.38E-12
vg1122937279 sf1122471150 11 22937279 5.86E-17 1.33E-12
vg0624774901 sf0624773904 6 24774901 2.27E-16 2.80E-10
vg0609657256 sf0609656257 6 9657256 1.22E-15 5.99E-10
vg1104144721 sf1104140623 11 4144721 1.67E-14 3.04E-08
vg1204614271 sf1204613259 12 4614271 1.78E-14 5.47E-08
vg0624696649 sf0624695652 6 24696649 3.71E-14 4.73E-11
vg1225764387 sf1225730781 12 25764387 5.77E-14 1.06E-09
vg0205557943 sf0205557943 2 5557943 1.88E-13 6.85E-08
vg0610197867 sf0610196868 6 10197867 2.26E-13 4.67E-10
vg0312772189 sf0312770907 3 12772189 6.60E-13 7.63E-10
vg0528796740 sf0528734095 5 28796740 1.76E-12 4.44E-08
vg1209813012 sf1209810422 12 9813012 3.16E-12 6.11E-08
vg0216375201 sf0216369331 2 16375201 4.54E-12 2.92E-08
vg0130082160 sf0130081115 1 30082160 1.02E-10 1.16E-08
vg0311212518 sf0311211236 3 11212518 1.54E-10 4.93E-09
vg0208996721 sf0208996719 2 8996721 2.49E-10 1.33E-08
vg1215688513 sf1215685810 12 15688513 7.42E-10 2.11E-08
vg0506412273 sf0506412212 5 6412273 2.24E-09 2.97E-08
vg0229293828 sf0229287959 2 29293828 1.67E-08 4.79E-09
vg1224760684 sf1224727138 12 24760684 3.14E-07 5.43E-08