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 mr1243 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
vg0216673252 sf0216667382 2 16673252 4.26E-62 5.62E-13
vg0216891914 sf0216886044 2 16891914 6.42E-60 4.15E-13
vg1101091696 sf1101090697 11 1091696 7.35E-47 NA
vg0128362507 sf0128361463 1 28362507 2.67E-45 NA
vg0304976705 sf0304975707 3 4976705 4.96E-45 NA
vg0205725551 sf0205725551 2 5725551 1.29E-44 NA
vg0526133789 sf0526071209 5 26133789 9.75E-40 1.27E-06
vg0317321849 sf0317320659 3 17321849 2.30E-39 2.17E-06
vg0217739410 sf0217733540 2 17739410 NA 2.38E-10
vg0318042099 sf0318040881 3 18042099 NA 1.22E-06
vg0706052872 sf0706051873 7 6052872 NA 4.63E-06
vg0213822496 sf0213816626 2 13822496 NA 4.78E-06
vg0416838478 sf0416666521 4 16838478 NA 4.96E-06