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 mr1982 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
vg0602541654 sf0602540655 6 2541654 5.49E-18 NA
vg0602598450 sf0602597451 6 2598450 1.42E-17 3.99E-06
vg0408318442 sf0408313716 4 8318442 3.24E-17 NA
vg1002389961 sf1002388938 10 2389961 1.18E-16 NA
vg0719005365 sf0719004372 7 19005365 1.19E-16 NA
vg0519644589 sf0519582073 5 19644589 2.05E-16 NA
vg1003625172 sf1003624149 10 3625172 4.74E-16 3.27E-06
vg0909181183 sf0909180182 9 9181183 1.63E-15 NA
vg1002906134 sf1002905111 10 2906134 1.68E-15 NA
vg0105170616 sf0105169616 1 5170616 6.09E-15 4.55E-06
vg1116818450 sf1116353328 11 16818450 1.98E-14 2.07E-06
vg0120188568 sf0120187523 1 20188568 2.71E-13 8.68E-06
vg0407766368 sf0407761636 4 7766368 NA 2.24E-06
vg0908536377 sf0908535376 9 8536377 NA 3.33E-06
vg1121947567 sf1121481438 11 21947567 NA 6.87E-06