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 mr1027 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
vg1005631054 sf1005647592 10 5631054 6.82E-13 4.96E-07
vg0412457585 sf0412448300 4 12457585 1.47E-11 5.87E-07
vg1008388235 sf1008317097 10 8388235 1.86E-11 8.83E-08
vg1006617495 sf1006633118 10 6617495 9.09E-11 1.39E-08
vg0134963133 sf0134962090 1 34963133 1.01E-10 NA
vg0403274963 sf0403270566 4 3274963 2.09E-10 6.22E-06
vg1006617462 sf1006633085 10 6617462 2.83E-10 1.27E-08
vg0713647697 sf0713646704 7 13647697 3.57E-10 7.94E-06
vg1009351636 sf1009280457 10 9351636 1.76E-09 1.71E-06
vg0133243522 sf0133242478 1 33243522 2.07E-09 2.40E-07
vg0231466195 sf0231460326 2 31466195 1.65E-08 1.64E-06
vg0913505389 sf0913504388 9 13505389 2.55E-07 NA
vg1109631523 sf1109626100 11 9631523 9.69E-06 NA
vg0511023890 sf0511023819 5 11023890 NA 4.92E-07
vg0331773900 sf0331766777 3 31773900 NA 4.16E-06
vg0404968530 sf0404963969 4 4968530 NA 4.19E-06