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 mr1524 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
vg0330500523 sf0330493412 3 30500523 3.68E-15 8.03E-06
vg0400008206 sf0400007206 4 8206 1.68E-13 NA
vg0522383666 sf0522321107 5 22383666 2.22E-13 NA
vg0715544956 sf0715543963 7 15544956 3.42E-13 NA
vg1016528653 sf1016457426 10 16528653 4.78E-13 NA
vg1122503071 sf1122036942 11 22503071 2.07E-10 7.82E-06
vg0317247368 sf0317246178 3 17247368 2.23E-10 4.27E-06
vg0712954506 sf0712953513 7 12954506 8.43E-10 9.98E-06
vg0330494102 sf0330486991 3 30494102 NA 4.26E-08
vg1104585220 sf1104581122 11 4585220 NA 4.31E-07
vg1216246100 sf1216243396 12 16246100 NA 1.75E-06
vg1215284390 sf1215281688 12 15284390 NA 2.77E-06