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 mr1648 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
vg0608189642 sf0608188643 6 8189642 1.02E-12 NA
vg0615854987 sf0615853989 6 15854987 2.33E-12 NA
vg0313958242 sf0313956959 3 13958242 2.51E-12 NA
vg0127819685 sf0127818641 1 27819685 2.62E-12 NA
vg0113332732 sf0113331706 1 13332732 3.02E-12 1.86E-07
vg0528383763 sf0528321118 5 28383763 8.64E-10 5.05E-06
vg1216556169 sf1216553462 12 16556169 1.02E-09 NA
vg0615274132 sf0615273133 6 15274132 4.01E-09 NA
vg0523610597 sf0523548018 5 23610597 8.03E-09 NA
vg0621526127 sf0621525130 6 21526127 7.42E-08 NA
vg0906793623 sf0906792623 9 6793623 NA 3.50E-09
vg0506138324 sf0506138263 5 6138324 NA 3.43E-07
vg0601158634 sf0601157635 6 1158634 NA 4.49E-07
vg0112449854 sf0112448828 1 12449854 NA 4.72E-07
vg0513518841 sf0513461388 5 13518841 NA 7.59E-07
vg0617070993 sf0617069996 6 17070993 NA 1.55E-06
vg0719531114 sf0719530121 7 19531114 NA 1.55E-06
vg1124506486 sf1124040326 11 24506486 NA 1.57E-06
vg1224680553 sf1224647007 12 24680553 NA 2.51E-06
vg0135233075 sf0135232032 1 35233075 NA 2.60E-06
vg0335905588 sf0335898457 3 35905588 NA 3.38E-06
vg0119206650 sf0119205605 1 19206650 NA 3.60E-06
vg1224680477 sf1224646931 12 24680477 NA 4.56E-06
vg0506481904 sf0506481845 5 6481904 NA 4.65E-06