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
vg0918496669 sf0918495668 9 18496669 5.01E-13 2.08E-10
vg0918923624 sf0918922624 9 18923624 2.04E-11 1.14E-10
vg1213036073 sf1213033412 12 13036073 1.88E-08 3.29E-06
vg0910545208 sf0910544207 9 10545208 2.97E-08 5.85E-07
vg0301666309 sf0301665305 3 1666309 3.43E-08 NA
vg0235063590 sf0235057721 2 35063590 4.34E-08 NA
vg1220855520 sf1220822069 12 20855520 6.10E-08 4.00E-06
vg1218068872 sf1218040308 12 18068872 5.37E-07 3.91E-06
vg0432816830 sf0432631716 4 32816830 2.02E-06 1.07E-06
vg1202071874 sf1202070872 12 2071874 NA 2.32E-06
vg1221003294 sf1220969844 12 21003294 NA 2.77E-06