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 mr1940 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
vg0820967741 sf0820965028 8 20967741 4.10E-14 6.76E-08
vg0820974361 sf0820971648 8 20974361 2.10E-13 6.23E-08
vg1219761908 sf1219733378 12 19761908 1.64E-12 1.39E-06
vg0433424538 sf0433239427 4 33424538 7.70E-12 NA
vg0802885223 sf0802884226 8 2885223 8.22E-12 NA
vg1215227521 sf1215224818 12 15227521 2.76E-11 NA
vg1005564150 sf1005580688 10 5564150 8.18E-11 NA
vg0421456232 sf0421284283 4 21456232 2.26E-09 4.95E-06
vg1216757238 sf1216751192 12 16757238 1.01E-08 NA
vg0323895857 sf0323894031 3 23895857 NA 7.36E-07
vg0315800734 sf0315799381 3 15800734 NA 7.43E-07
vg0523035315 sf0522972756 5 23035315 NA 2.38E-06
vg0525640092 sf0525577513 5 25640092 NA 3.43E-06
vg0904506888 sf0904505888 9 4506888 NA 3.52E-06