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 mr1653 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
vg0131754198 sf0131753154 1 31754198 2.12E-14 NA
vg0123720143 sf0123719099 1 23720143 1.12E-12 NA
vg0138424728 sf0138423685 1 38424728 1.59E-12 NA
vg0728880405 sf0728879413 7 28880405 5.14E-12 NA
vg0726964336 sf0726963342 7 26964336 9.00E-12 NA
vg0523663962 sf0523601383 5 23663962 8.14E-11 NA
vg0123691889 sf0123690845 1 23691889 3.98E-08 NA
vg0807847137 sf0807846141 8 7847137 NA 1.55E-06