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 mr1342 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
vg0232755756 sf0232749887 2 32755756 1.15E-21 6.57E-08
vg0917808340 sf0917807339 9 17808340 2.39E-21 4.36E-06
vg0228204274 sf0228198405 2 28204274 3.82E-21 1.44E-07
vg0914839744 sf0914838743 9 14839744 5.49E-20 NA
vg0706556372 sf0706555377 7 6556372 7.20E-20 NA
vg0417591194 sf0417419235 4 17591194 NA 1.82E-06
vg0416719847 sf0416547891 4 16719847 NA 2.58E-06
vg0608071648 sf0608070649 6 8071648 NA 3.23E-06
vg0421022330 sf0420850383 4 21022330 NA 3.48E-06
vg0416770811 sf0416598855 4 16770811 NA 4.25E-06