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 mr1961 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
vg1001348300 sf1001347277 10 1348300 5.76E-12 2.19E-09
vg0219292377 sf0219286509 2 19292377 1.54E-09 1.05E-06
vg0316353556 sf0316352203 3 16353556 1.82E-09 2.56E-06
vg0424049928 sf0423864789 4 24049928 2.92E-09 1.91E-07
vg1021101017 sf1021029496 10 21101017 4.24E-09 5.31E-06
vg0504720198 sf0504720175 5 4720198 5.11E-09 5.51E-07
vg0336193973 sf0336186899 3 36193973 5.13E-09 2.93E-07
vg0819366916 sf0819364203 8 19366916 1.75E-08 6.21E-07
vg0403207821 sf0403203424 4 3207821 1.96E-08 3.57E-08
vg0728000317 sf0727999324 7 28000317 2.81E-08 7.58E-07
vg1018998670 sf1018927227 10 18998670 3.47E-08 1.78E-06
vg0918474400 sf0918473399 9 18474400 1.48E-07 4.60E-06
vg0308535729 sf0308534667 3 8535729 3.38E-07 4.67E-06
vg0421387824 sf0421215877 4 21387824 4.90E-07 2.12E-06
vg1117137503 sf1116671355 11 17137503 9.00E-07 1.69E-06
vg1205542061 sf1205541047 12 5542061 1.10E-06 3.89E-06
vg0807204233 sf0807203238 8 7204233 1.34E-06 3.42E-06
vg1209218924 sf1209216333 12 9218924 4.89E-06 3.66E-06
vg0136191693 sf0136190650 1 36191693 NA 4.22E-06