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 mr1506 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
vg1219850678 sf1219822148 12 19850678 1.49E-13 4.75E-06
vg0724945438 sf0724944444 7 24945438 3.24E-13 1.53E-06
vg0140420434 sf0140419391 1 40420434 3.95E-13 8.54E-06
vg0921976011 sf0921975530 9 21976011 5.96E-13 NA
vg0230082625 sf0230076756 2 30082625 9.11E-13 NA
vg0902107236 sf0902106236 9 2107236 1.08E-12 2.17E-07
vg0805992743 sf0805991746 8 5992743 1.20E-12 1.19E-07
vg0915815139 sf0915814138 9 15815139 2.51E-12 3.00E-06
vg0528836237 sf0528773592 5 28836237 8.07E-12 2.39E-06
vg0335297514 sf0335290383 3 35297514 8.19E-12 1.62E-06
vg0133432014 sf0133430970 1 33432014 5.62E-11 3.09E-06
vg1118023722 sf1117557580 11 18023722 1.66E-10 2.51E-06
vg0724610432 sf0724609438 7 24610432 NA 3.04E-06
vg0104557963 sf0104556963 1 4557963 NA 4.00E-06