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 mr1067 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
vg0610587294 sf0610586295 6 10587294 1.27E-91 7.70E-29
vg0610558074 sf0610557075 6 10558074 4.83E-87 3.13E-25
vg0222746228 sf0222740359 2 22746228 3.67E-74 1.40E-18
vg0610363238 sf0610362239 6 10363238 1.74E-71 1.48E-15
vg0616950705 sf0616949708 6 16950705 3.54E-71 NA
vg0719132379 sf0719131386 7 19132379 9.11E-68 NA
vg0122580922 sf0122579877 1 22580922 6.80E-67 NA
vg0222719698 sf0222713829 2 22719698 5.99E-62 1.37E-25
vg0719492802 sf0719491809 7 19492802 1.23E-55 5.22E-07
vg0610763769 sf0610762770 6 10763769 NA 1.31E-11
vg0222743085 sf0222737216 2 22743085 NA 2.16E-11
vg0609919357 sf0609918358 6 9919357 NA 3.33E-11
vg0610487099 sf0610486100 6 10487099 NA 1.43E-10
vg0609929059 sf0609928060 6 9929059 NA 1.14E-08
vg0222573327 sf0222567458 2 22573327 NA 1.20E-08
vg0223051444 sf0223045575 2 23051444 NA 1.92E-08
vg0224274396 sf0224268527 2 24274396 NA 8.71E-08
vg0610878296 sf0610877297 6 10878296 NA 9.02E-08
vg0610421019 sf0610420020 6 10421019 NA 1.25E-07
vg0222729853 sf0222723984 2 22729853 NA 1.51E-07
vg0611682950 sf0611681951 6 11682950 NA 2.71E-07
vg0719505903 sf0719504910 7 19505903 NA 3.48E-07
vg0610444069 sf0610443070 6 10444069 NA 6.83E-07
vg0610417183 sf0610416184 6 10417183 NA 7.19E-07
vg0223699215 sf0223693346 2 23699215 NA 8.96E-07
vg0611926589 sf0611925590 6 11926589 NA 1.19E-06
vg0306622337 sf0306621337 3 6622337 NA 1.19E-06
vg0610393322 sf0610392323 6 10393322 NA 1.20E-06
vg0617829118 sf0617828121 6 17829118 NA 1.29E-06
vg0610730985 sf0610729986 6 10730985 NA 2.70E-06
vg0506761860 sf0506761802 5 6761860 NA 3.01E-06
vg0610014317 sf0610013318 6 10014317 NA 4.44E-06
vg0617826591 sf0617825594 6 17826591 NA 4.73E-06