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 mr1091 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
vg0610559165 sf0610558166 6 10559165 1.50E-110 1.07E-36
vg0610585146 sf0610584147 6 10585146 1.15E-84 1.03E-29
vg0617223679 sf0617222682 6 17223679 1.53E-64 4.96E-12
vg0614652165 sf0614651166 6 14652165 1.17E-57 2.16E-08
vg0719209059 sf0719208066 7 19209059 1.54E-52 NA
vg0711372433 sf0711371439 7 11372433 5.80E-47 NA
vg0629122299 sf0629121301 6 29122299 3.68E-46 1.94E-07
vg0718862824 sf0718861831 7 18862824 1.42E-42 1.22E-06
vg0610763769 sf0610762770 6 10763769 NA 9.72E-16
vg0610476284 sf0610475285 6 10476284 NA 9.89E-14
vg0611863008 sf0611862009 6 11863008 NA 4.70E-11
vg0611682950 sf0611681951 6 11682950 NA 5.46E-11
vg0609930953 sf0609929954 6 9930953 NA 5.93E-11
vg0610000286 sf0609999287 6 10000286 NA 4.30E-10
vg0610441964 sf0610440965 6 10441964 NA 4.69E-10
vg0610813890 sf0610812891 6 10813890 NA 5.07E-10
vg0610014317 sf0610013318 6 10014317 NA 1.73E-09
vg0611002115 sf0611001116 6 11002115 NA 2.08E-09
vg0610788748 sf0610787749 6 10788748 NA 1.45E-08
vg0610393322 sf0610392323 6 10393322 NA 5.65E-08
vg0614785443 sf0614784444 6 14785443 NA 1.26E-07
vg0609643486 sf0609642487 6 9643486 NA 1.42E-07
vg0610149647 sf0610148648 6 10149647 NA 2.62E-07