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 mr1232 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
vg0918936020 sf0918935020 9 18936020 1.51E-17 6.09E-08
vg0301666309 sf0301665305 3 1666309 4.94E-17 NA
vg1218097299 sf1218068735 12 18097299 3.18E-15 NA
vg0422543641 sf0422358528 4 22543641 6.36E-15 8.97E-06
vg0327563081 sf0327556134 3 27563081 1.58E-14 NA
vg0422994391 sf0422809283 4 22994391 1.48E-13 1.53E-06
vg0526297588 sf0526234951 5 26297588 2.76E-11 3.41E-06
vg0918496669 sf0918495668 9 18496669 2.47E-10 3.16E-09
vg1102473089 sf1102468993 11 2473089 4.44E-10 4.10E-06
vg0918924003 sf0918923003 9 18924003 NA 8.80E-11
vg0224432257 sf0224426388 2 24432257 NA 1.51E-07
vg1218068872 sf1218040308 12 18068872 NA 3.05E-06
vg1220855520 sf1220822069 12 20855520 NA 5.33E-06